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, 36 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p33 cnv correlated to 'CN_CNMF'.

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

  • amp_19p13.2 cnv correlated to 'CN_CNMF'.

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

  • del_3p13 cnv correlated to 'CN_CNMF'.

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

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

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

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

  • del_12p13.2 cnv correlated to 'CN_CNMF'.

  • del_12q21.33 cnv correlated to 'CN_CNMF'.

  • del_16q23.1 cnv correlated to 'CN_CNMF'.

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

  • del_17q11.2 cnv correlated to 'CN_CNMF'.

  • del_18p11.21 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, 36 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
(0.00116) 		9e-05
(0.00909) 		0.00534
(0.406) 		0.00084
(0.0764) 		0.00077
(0.0716) 		0.0013
(0.112)
del 7q34 24 (13%) 167 1e-05
(0.00116) 		6e-05
(0.00618) 		0.0215
(1.00) 		1e-05
(0.00116) 		0.0008
(0.0736) 		0.00055
(0.0533)
del 7q34 24 (13%) 167 1e-05
(0.00116) 		6e-05
(0.00618) 		0.0216
(1.00) 		2e-05
(0.00216) 		0.00092
(0.0819) 		0.00056
(0.0538)
del 7p12 1 16 (8%) 175 0.00019
(0.019) 		0.00062
(0.0589) 		0.00186
(0.154) 		5e-05
(0.0052) 		0.00614
(0.454) 		0.00639
(0.46)
del 17p13 2 15 (8%) 176 1e-05
(0.00116) 		0.00085
(0.0765) 		0.0114
(0.767) 		0.0002
(0.0198) 		0.0865
(1.00) 		0.00116
(0.102)
amp 21q22 2 14 (7%) 177 1e-05
(0.00116) 		0.00214
(0.175) 		0.00327
(0.262) 		0.0361
(1.00) 		0.00167
(0.14) 		0.0673
(1.00)
amp 11q23 3 17 (9%) 174 1e-05
(0.00116) 		2e-05
(0.00216) 		0.373
(1.00) 		0.201
(1.00) 		0.746
(1.00) 		0.187
(1.00)
amp 1p33 7 (4%) 184 0.00049
(0.048) 		0.0116
(0.767) 		0.125
(1.00) 		0.13
(1.00) 		0.00951
(0.656) 		0.0492
(1.00)
amp 19p13 2 6 (3%) 185 0.0029
(0.235) 		0.555
(1.00) 		0.857
(1.00) 		0.632
(1.00) 		0.895
(1.00) 		1
(1.00)
del 3p13 8 (4%) 183 0.00072
(0.0677) 		0.297
(1.00) 		0.0676
(1.00) 		0.236
(1.00) 		0.0365
(1.00) 		0.0478
(1.00)
del 12p13 2 10 (5%) 181 2e-05
(0.00216) 		0.00519
(0.4) 		0.199
(1.00) 		0.0723
(1.00) 		0.0697
(1.00) 		0.00959
(0.656)
del 12q21 33 3 (2%) 188 0.00135
(0.115) 		0.304
(1.00) 		0.187
(1.00) 		0.587
(1.00) 		0.00843
(0.59) 		0.006
(0.45)
del 16q23 1 9 (5%) 182 0.00121
(0.105) 		0.149
(1.00) 		0.33
(1.00) 		0.494
(1.00) 		0.043
(1.00) 		0.0657
(1.00)
del 17q11 2 13 (7%) 178 1e-05
(0.00116) 		0.0224
(1.00) 		0.156
(1.00) 		0.00661
(0.469) 		0.136
(1.00) 		0.0035
(0.273)
del 18p11 21 9 (5%) 182 2e-05
(0.00216) 		0.0178
(1.00) 		0.382
(1.00) 		0.335
(1.00) 		0.213
(1.00) 		0.0311
(1.00)
amp 1q43 7 (4%) 184 0.00338
(0.267) 		0.0124
(0.808) 		0.377
(1.00) 		0.0364
(1.00) 		0.137
(1.00) 		0.015
(0.944)
amp 13q31 3 7 (4%) 184 0.0807
(1.00) 		0.0124
(0.808) 		0.067
(1.00) 		0.0364
(1.00) 		0.737
(1.00) 		0.0566
(1.00)
amp 20q11 21 3 (2%) 188 0.00618
(0.454) 		0.267
(1.00)
del 9q21 32 5 (3%) 186 0.236
(1.00) 		0.516
(1.00) 		0.176
(1.00) 		0.602
(1.00) 		0.182
(1.00) 		0.105
(1.00)
del 20q13 13 4 (2%) 187 0.0288
(1.00) 		0.148
(1.00) 		0.787
(1.00) 		0.588
(1.00) 		0.126
(1.00) 		0.411
(1.00)
'amp_1p33' versus 'CN_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.048

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_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S2.  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 S2.  Get High-res Image Gene #3: 'amp_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q23.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0022

Table S3.  Gene #3: 'amp_11q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 61 14 20
AMP PEAK 3(11Q23.3) MUTATED 0 0 12 4 1
AMP PEAK 3(11Q23.3) WILD-TYPE 46 44 49 10 19

Figure S3.  Get High-res Image Gene #3: 'amp_11q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'CN_CNMF'

P value = 0.0029 (Fisher's exact test), Q value = 0.23

Table S4.  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 S4.  Get High-res Image Gene #5: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_21q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S5.  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 S5.  Get High-res Image Gene #7: 'amp_21q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_21q22.2' versus 'METHLYATION_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.18

Table S6.  Gene #7: 'amp_21q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 61 14 20
AMP PEAK 7(21Q22.2) MUTATED 1 0 11 0 1
AMP PEAK 7(21Q22.2) WILD-TYPE 45 44 50 14 19

Figure S6.  Get High-res Image Gene #7: 'amp_21q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_21q22.2' versus 'MIRSEQ_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.14

Table S7.  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 S7.  Get High-res Image Gene #7: 'amp_21q22.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p13' versus 'CN_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.068

Table S8.  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 S8.  Get High-res Image Gene #8: 'del_3p13' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S9.  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 S9.  Get High-res Image Gene #9: 'del_5q31.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q31.2' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0091

Table S10.  Gene #9: 'del_5q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 61 14 20
DEL PEAK 3(5Q31.2) MUTATED 1 0 15 0 2
DEL PEAK 3(5Q31.2) WILD-TYPE 45 44 46 14 18

Figure S10.  Get High-res Image Gene #9: 'del_5q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.076

Table S11.  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 S11.  Get High-res Image Gene #9: 'del_5q31.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_5q31.2' versus 'MIRSEQ_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.072

Table S12.  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 S12.  Get High-res Image Gene #9: 'del_5q31.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_5q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0013 (Fisher's exact test), Q value = 0.11

Table S13.  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 S13.  Get High-res Image Gene #9: 'del_5q31.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_7p12.1' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.019

Table S14.  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 S14.  Get High-res Image Gene #10: 'del_7p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7p12.1' versus 'METHLYATION_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.059

Table S15.  Gene #10: 'del_7p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 61 14 20
DEL PEAK 4(7P12.1) MUTATED 1 0 13 1 1
DEL PEAK 4(7P12.1) WILD-TYPE 45 44 48 13 19

Figure S15.  Get High-res Image Gene #10: 'del_7p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00186 (Fisher's exact test), Q value = 0.15

Table S16.  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 S16.  Get High-res Image Gene #10: 'del_7p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_7p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.0052

Table S17.  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 S17.  Get High-res Image Gene #10: 'del_7p12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_7q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S18.  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 S18.  Get High-res Image Gene #11: 'del_7q34' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q34' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0062

Table S19.  Gene #11: 'del_7q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 61 14 20
DEL PEAK 5(7Q34) MUTATED 1 1 18 2 2
DEL PEAK 5(7Q34) WILD-TYPE 45 43 43 12 18

Figure S19.  Get High-res Image Gene #11: 'del_7q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S20.  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 S20.  Get High-res Image Gene #11: 'del_7q34' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_7q34' versus 'MIRSEQ_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.074

Table S21.  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 S21.  Get High-res Image Gene #11: 'del_7q34' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_7q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.053

Table S22.  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 S22.  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 = 0.0012

Table S23.  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 S23.  Get High-res Image Gene #12: 'del_7q34' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q34' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0062

Table S24.  Gene #12: 'del_7q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 61 14 20
DEL PEAK 6(7Q34) MUTATED 1 1 18 2 2
DEL PEAK 6(7Q34) WILD-TYPE 45 43 43 12 18

Figure S24.  Get High-res Image Gene #12: 'del_7q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0022

Table S25.  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 S25.  Get High-res Image Gene #12: 'del_7q34' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_7q34' versus 'MIRSEQ_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.082

Table S26.  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 S26.  Get High-res Image Gene #12: 'del_7q34' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_7q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.054

Table S27.  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 S27.  Get High-res Image Gene #12: 'del_7q34' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0022

Table S28.  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 S28.  Get High-res Image Gene #14: 'del_12p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q21.33' versus 'CN_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.11

Table S29.  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 S29.  Get High-res Image Gene #15: 'del_12q21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.11

Table S30.  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 S30.  Get High-res Image Gene #16: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S31.  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 S31.  Get High-res Image Gene #17: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.2' versus 'METHLYATION_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.076

Table S32.  Gene #17: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 61 14 20
DEL PEAK 13(17P13.2) MUTATED 0 1 12 0 2
DEL PEAK 13(17P13.2) WILD-TYPE 46 43 49 14 18

Figure S32.  Get High-res Image Gene #17: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.02

Table S33.  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 S33.  Get High-res Image Gene #17: 'del_17p13.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00116 (Fisher's exact test), Q value = 0.1

Table S34.  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 S34.  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 = 0.0012

Table S35.  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 S35.  Get High-res Image Gene #18: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18p11.21' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0022

Table S36.  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 S36.  Get High-res Image Gene #19: 'del_18p11.21' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

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

  • Molecular subtype file = 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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