This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 21 focal events and 6 molecular subtypes across 191 patients, 33 significant findings detected with P value < 0.05 and Q value < 0.25.
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amp_1p33 cnv correlated to 'CN_CNMF'.
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amp_11q23.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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amp_19p13.2 cnv correlated to 'CN_CNMF'.
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amp_21q22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
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del_3p13 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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del_5q31.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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del_7p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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del_7q32.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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del_7q34 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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del_12p13.2 cnv correlated to 'CN_CNMF'.
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del_12q21.33 cnv correlated to 'CN_CNMF'.
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del_16q23.1 cnv correlated to 'CN_CNMF'.
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del_17p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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del_17q11.2 cnv correlated to 'CN_CNMF'.
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del_18p11.21 cnv correlated to 'CN_CNMF'.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
del 7p12 1 | 16 (8%) | 175 |
0.0004 (0.0424) |
0.000667 (0.0693) |
0.00172 (0.163) |
0.00272 (0.247) |
0.00598 (0.496) |
0.00167 (0.161) |
del 5q31 2 | 18 (9%) | 173 |
1.77e-13 (2.14e-11) |
6.11e-05 (0.0069) |
0.00512 (0.445) |
0.0923 (1.00) |
0.000865 (0.0882) |
0.000478 (0.0502) |
del 7q34 | 24 (13%) | 167 |
6.26e-07 (7.39e-05) |
7.4e-05 (0.00829) |
0.0212 (1.00) |
0.0212 (1.00) |
0.00105 (0.106) |
2.31e-05 (0.00264) |
amp 21q22 2 | 14 (7%) | 177 |
5.15e-13 (6.17e-11) |
0.00156 (0.153) |
0.00336 (0.299) |
0.337 (1.00) |
0.00177 (0.167) |
0.0173 (1.00) |
del 7q32 3 | 23 (12%) | 168 |
2.38e-07 (2.84e-05) |
0.000189 (0.0203) |
0.0374 (1.00) |
0.022 (1.00) |
0.00295 (0.265) |
9.24e-05 (0.0102) |
del 17p13 2 | 15 (8%) | 176 |
1.4e-14 (1.71e-12) |
0.00105 (0.106) |
0.0106 (0.782) |
0.0211 (1.00) |
0.087 (1.00) |
0.00141 (0.14) |
amp 11q23 3 | 17 (9%) | 174 |
8.57e-21 (1.05e-18) |
8.51e-05 (0.00944) |
0.358 (1.00) |
0.784 (1.00) |
0.746 (1.00) |
0.915 (1.00) |
del 3p13 | 9 (5%) | 182 |
0.00015 (0.0163) |
0.137 (1.00) |
0.0349 (1.00) |
0.718 (1.00) |
0.012 (0.878) |
0.00166 (0.161) |
amp 1p33 | 7 (4%) | 184 |
0.000671 (0.0693) |
0.00516 (0.445) |
0.124 (1.00) |
0.665 (1.00) |
0.00989 (0.741) |
0.23 (1.00) |
amp 19p13 2 | 6 (3%) | 185 |
0.000137 (0.0149) |
0.581 (1.00) |
0.857 (1.00) |
0.664 (1.00) |
0.895 (1.00) |
0.863 (1.00) |
del 12p13 2 | 10 (5%) | 181 |
2.12e-05 (0.00243) |
0.00776 (0.621) |
0.197 (1.00) |
0.167 (1.00) |
0.0682 (1.00) |
0.0217 (1.00) |
del 12q21 33 | 3 (2%) | 188 |
0.00197 (0.181) |
0.38 (1.00) |
0.186 (1.00) |
0.552 (1.00) |
0.00827 (0.645) |
0.00696 (0.571) |
del 16q23 1 | 9 (5%) | 182 |
0.00182 (0.169) |
0.0648 (1.00) |
0.332 (1.00) |
1 (1.00) |
0.0442 (1.00) |
0.0493 (1.00) |
del 17q11 2 | 13 (7%) | 178 |
1.33e-06 (0.000155) |
0.029 (1.00) |
0.151 (1.00) |
0.222 (1.00) |
0.136 (1.00) |
0.00924 (0.702) |
del 18p11 21 | 9 (5%) | 182 |
3.46e-06 (0.000401) |
0.00832 (0.645) |
0.381 (1.00) |
0.718 (1.00) |
0.213 (1.00) |
0.0914 (1.00) |
amp 1q43 | 7 (4%) | 184 |
0.0047 (0.413) |
0.00516 (0.445) |
0.373 (1.00) |
0.425 (1.00) |
0.137 (1.00) |
0.121 (1.00) |
amp 13q31 3 | 7 (4%) | 184 |
0.0849 (1.00) |
0.00516 (0.445) |
0.0668 (1.00) |
0.0965 (1.00) |
0.735 (1.00) |
0.143 (1.00) |
amp 20q11 21 | 3 (2%) | 188 |
0.00767 (0.621) |
0.185 (1.00) |
0.55 (1.00) |
|||
del 3q26 31 | 3 (2%) | 188 |
0.00767 (0.621) |
0.185 (1.00) |
0.786 (1.00) |
1 (1.00) |
0.0618 (1.00) |
0.0481 (1.00) |
del 9q21 32 | 5 (3%) | 186 |
0.256 (1.00) |
0.416 (1.00) |
0.176 (1.00) |
0.664 (1.00) |
0.183 (1.00) |
0.108 (1.00) |
del 20q13 13 | 4 (2%) | 187 |
0.0259 (1.00) |
0.0808 (1.00) |
0.786 (1.00) |
1 (1.00) |
0.125 (1.00) |
0.222 (1.00) |
P value = 0.000671 (Fisher's exact test), Q value = 0.069
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
AMP PEAK 1(1P33) MUTATED | 1 | 3 | 3 | 0 |
AMP PEAK 1(1P33) WILD-TYPE | 146 | 11 | 24 | 3 |
P value = 8.57e-21 (Fisher's exact test), Q value = 1.1e-18
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
AMP PEAK 3(11Q23.3) MUTATED | 0 | 14 | 3 | 0 |
AMP PEAK 3(11Q23.3) WILD-TYPE | 147 | 0 | 24 | 3 |
P value = 8.51e-05 (Chi-square test), Q value = 0.0094
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 |
P value = 0.000137 (Fisher's exact test), Q value = 0.015
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
AMP PEAK 5(19P13.2) MUTATED | 0 | 1 | 5 | 0 |
AMP PEAK 5(19P13.2) WILD-TYPE | 147 | 13 | 22 | 3 |
P value = 5.15e-13 (Fisher's exact test), Q value = 6.2e-11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
AMP PEAK 7(21Q22.2) MUTATED | 0 | 0 | 13 | 1 |
AMP PEAK 7(21Q22.2) WILD-TYPE | 147 | 14 | 14 | 2 |
P value = 0.00156 (Chi-square test), Q value = 0.15
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 |
P value = 0.00177 (Fisher's exact test), Q value = 0.17
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 |
P value = 0.00015 (Fisher's exact test), Q value = 0.016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
DEL PEAK 2(3P13) MUTATED | 2 | 0 | 7 | 0 |
DEL PEAK 2(3P13) WILD-TYPE | 145 | 14 | 20 | 3 |
P value = 0.00166 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 79 | 65 |
DEL PEAK 2(3P13) MUTATED | 5 | 0 | 3 |
DEL PEAK 2(3P13) WILD-TYPE | 30 | 79 | 62 |
P value = 1.77e-13 (Fisher's exact test), Q value = 2.1e-11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
DEL PEAK 4(5Q31.2) MUTATED | 1 | 1 | 15 | 1 |
DEL PEAK 4(5Q31.2) WILD-TYPE | 146 | 13 | 12 | 2 |
P value = 6.11e-05 (Chi-square test), Q value = 0.0069
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 46 | 44 | 61 | 14 | 20 |
DEL PEAK 4(5Q31.2) MUTATED | 1 | 0 | 15 | 0 | 2 |
DEL PEAK 4(5Q31.2) WILD-TYPE | 45 | 44 | 46 | 14 | 18 |
P value = 0.000865 (Fisher's exact test), Q value = 0.088
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 37 | 41 | 43 |
DEL PEAK 4(5Q31.2) MUTATED | 1 | 10 | 3 | 3 |
DEL PEAK 4(5Q31.2) WILD-TYPE | 57 | 27 | 38 | 40 |
P value = 0.000478 (Fisher's exact test), Q value = 0.05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 79 | 65 |
DEL PEAK 4(5Q31.2) MUTATED | 10 | 3 | 4 |
DEL PEAK 4(5Q31.2) WILD-TYPE | 25 | 76 | 61 |
P value = 4e-04 (Fisher's exact test), Q value = 0.042
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
DEL PEAK 5(7P12.1) MUTATED | 7 | 0 | 8 | 1 |
DEL PEAK 5(7P12.1) WILD-TYPE | 140 | 14 | 19 | 2 |
P value = 0.000667 (Chi-square test), Q value = 0.069
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 46 | 44 | 61 | 14 | 20 |
DEL PEAK 5(7P12.1) MUTATED | 1 | 0 | 13 | 1 | 1 |
DEL PEAK 5(7P12.1) WILD-TYPE | 45 | 44 | 48 | 13 | 19 |
P value = 0.00172 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 70 | 52 | 44 |
DEL PEAK 5(7P12.1) MUTATED | 12 | 0 | 3 |
DEL PEAK 5(7P12.1) WILD-TYPE | 58 | 52 | 41 |
P value = 0.00272 (Fisher's exact test), Q value = 0.25
nPatients | CLUS_1 | CLUS_2 |
---|---|---|
ALL | 56 | 110 |
DEL PEAK 5(7P12.1) MUTATED | 0 | 15 |
DEL PEAK 5(7P12.1) WILD-TYPE | 56 | 95 |
P value = 0.00167 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 79 | 65 |
DEL PEAK 5(7P12.1) MUTATED | 9 | 3 | 4 |
DEL PEAK 5(7P12.1) WILD-TYPE | 26 | 76 | 61 |
P value = 2.38e-07 (Fisher's exact test), Q value = 2.8e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
DEL PEAK 6(7Q32.3) MUTATED | 8 | 2 | 10 | 3 |
DEL PEAK 6(7Q32.3) WILD-TYPE | 139 | 12 | 17 | 0 |
P value = 0.000189 (Chi-square test), Q value = 0.02
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 46 | 44 | 61 | 14 | 20 |
DEL PEAK 6(7Q32.3) MUTATED | 1 | 1 | 17 | 2 | 2 |
DEL PEAK 6(7Q32.3) WILD-TYPE | 45 | 43 | 44 | 12 | 18 |
P value = 9.24e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 79 | 65 |
DEL PEAK 6(7Q32.3) MUTATED | 12 | 3 | 7 |
DEL PEAK 6(7Q32.3) WILD-TYPE | 23 | 76 | 58 |
P value = 6.26e-07 (Fisher's exact test), Q value = 7.4e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
DEL PEAK 7(7Q34) MUTATED | 9 | 2 | 10 | 3 |
DEL PEAK 7(7Q34) WILD-TYPE | 138 | 12 | 17 | 0 |
P value = 7.4e-05 (Chi-square test), Q value = 0.0083
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 46 | 44 | 61 | 14 | 20 |
DEL PEAK 7(7Q34) MUTATED | 1 | 1 | 18 | 2 | 2 |
DEL PEAK 7(7Q34) WILD-TYPE | 45 | 43 | 43 | 12 | 18 |
P value = 0.00105 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 37 | 41 | 43 |
DEL PEAK 7(7Q34) MUTATED | 2 | 12 | 5 | 4 |
DEL PEAK 7(7Q34) WILD-TYPE | 56 | 25 | 36 | 39 |
P value = 2.31e-05 (Fisher's exact test), Q value = 0.0026
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 79 | 65 |
DEL PEAK 7(7Q34) MUTATED | 13 | 3 | 7 |
DEL PEAK 7(7Q34) WILD-TYPE | 22 | 76 | 58 |
P value = 2.12e-05 (Fisher's exact test), Q value = 0.0024
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
DEL PEAK 10(12P13.2) MUTATED | 2 | 0 | 7 | 1 |
DEL PEAK 10(12P13.2) WILD-TYPE | 145 | 14 | 20 | 2 |
P value = 0.00197 (Fisher's exact test), Q value = 0.18
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
DEL PEAK 11(12Q21.33) MUTATED | 0 | 0 | 2 | 1 |
DEL PEAK 11(12Q21.33) WILD-TYPE | 147 | 14 | 25 | 2 |
P value = 0.00182 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
DEL PEAK 12(16Q23.1) MUTATED | 3 | 0 | 6 | 0 |
DEL PEAK 12(16Q23.1) WILD-TYPE | 144 | 14 | 21 | 3 |
P value = 1.4e-14 (Fisher's exact test), Q value = 1.7e-12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
DEL PEAK 13(17P13.2) MUTATED | 0 | 0 | 15 | 0 |
DEL PEAK 13(17P13.2) WILD-TYPE | 147 | 14 | 12 | 3 |
P value = 0.00105 (Chi-square test), Q value = 0.11
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 |
P value = 0.00141 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 79 | 65 |
DEL PEAK 13(17P13.2) MUTATED | 7 | 1 | 7 |
DEL PEAK 13(17P13.2) WILD-TYPE | 28 | 78 | 58 |
P value = 1.33e-06 (Fisher's exact test), Q value = 0.00016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
DEL PEAK 14(17Q11.2) MUTATED | 2 | 2 | 9 | 0 |
DEL PEAK 14(17Q11.2) WILD-TYPE | 145 | 12 | 18 | 3 |
P value = 3.46e-06 (Fisher's exact test), Q value = 4e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
DEL PEAK 15(18P11.21) MUTATED | 1 | 0 | 8 | 0 |
DEL PEAK 15(18P11.21) WILD-TYPE | 146 | 14 | 19 | 3 |
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Copy number data file = transformed.cor.cli.txt
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Molecular subtype file = LAML-TB.transferedmergedcluster.txt
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Number of patients = 191
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Number of significantly focal cnvs = 21
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Number of molecular subtypes = 6
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Exclude genes that fewer than K tumors have alterations, K = 3
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
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
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.
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.