(primary blood tumor (peripheral) cohort)
This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.
Testing the association between copy number variation of 20 peak regions and 6 molecular subtypes across 191 patients, 38 significant findings detected with Q value < 0.25.
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Amp Peak 1(1p33) cnvs correlated to 'CN_CNMF'.
-
Amp Peak 2(1q43) cnvs correlated to 'METHLYATION_CNMF'.
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Amp Peak 3(11q23.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 4(13q31.3) cnvs correlated to 'CN_CNMF'.
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Amp Peak 5(20q11.21) cnvs correlated to 'CN_CNMF'.
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Amp Peak 6(21q22.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 2(3p13) cnvs correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 4(5q31.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 5(7p12.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 6(7q32.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 7(7q34) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 10(12p13.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 12(16q23.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 13(17p13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 14(17q11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 15(18p11.21) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 16(20q13.13) cnvs correlated to 'CN_CNMF'.
Molecular subtypes |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ 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 | |
Del Peak 4(5q31 2) | 18 (9%) | 173 |
6.32e-15 (7.27e-13) |
5.31e-07 (5.62e-05) |
0.0053 (0.397) |
0.0923 (1.00) |
0.00131 (0.117) |
0.000764 (0.0702) |
Del Peak 5(7p12 1) | 16 (8%) | 175 |
2.4e-07 (2.64e-05) |
1.06e-05 (0.00108) |
0.00179 (0.152) |
0.00272 (0.217) |
0.0046 (0.349) |
0.0037 (0.285) |
Del Peak 6(7q32 3) | 23 (12%) | 168 |
8.78e-07 (9.22e-05) |
1.44e-05 (0.00145) |
0.0384 (1.00) |
0.022 (1.00) |
0.000422 (0.0401) |
0.000296 (0.0284) |
Del Peak 7(7q34) | 24 (13%) | 167 |
2.83e-06 (0.000295) |
3.61e-06 (0.000372) |
0.0221 (1.00) |
0.0212 (1.00) |
9.94e-05 (0.00965) |
8.56e-05 (0.00839) |
Del Peak 2(3p13) | 9 (5%) | 182 |
0.00179 (0.152) |
0.0384 (1.00) |
0.0349 (1.00) |
0.718 (1.00) |
0.00258 (0.209) |
0.00208 (0.173) |
Del Peak 13(17p13 2) | 15 (8%) | 176 |
1.68e-14 (1.91e-12) |
2.27e-05 (0.00225) |
0.0113 (0.754) |
0.0211 (1.00) |
0.0476 (1.00) |
0.00175 (0.15) |
Amp Peak 3(11q23 3) | 17 (9%) | 174 |
4.87e-33 (5.7e-31) |
0.00119 (0.107) |
0.373 (1.00) |
0.784 (1.00) |
1 (1.00) |
0.847 (1.00) |
Amp Peak 6(21q22 2) | 14 (7%) | 177 |
9.35e-32 (1.08e-29) |
0.000948 (0.0862) |
0.00336 (0.265) |
0.337 (1.00) |
0.0107 (0.726) |
0.0185 (1.00) |
Del Peak 10(12p13 2) | 10 (5%) | 181 |
8.25e-13 (9.33e-11) |
0.0022 (0.18) |
0.197 (1.00) |
0.167 (1.00) |
0.0962 (1.00) |
0.0241 (1.00) |
Del Peak 14(17q11 2) | 13 (7%) | 178 |
1.72e-05 (0.00172) |
0.00138 (0.12) |
0.156 (1.00) |
0.222 (1.00) |
0.154 (1.00) |
0.0093 (0.657) |
Del Peak 15(18p11 21) | 9 (5%) | 182 |
4.63e-07 (5e-05) |
0.000742 (0.069) |
0.381 (1.00) |
0.718 (1.00) |
0.149 (1.00) |
0.0974 (1.00) |
Amp Peak 1(1p33) | 7 (4%) | 184 |
4.86e-07 (5.2e-05) |
0.00924 (0.657) |
0.124 (1.00) |
0.665 (1.00) |
0.111 (1.00) |
0.238 (1.00) |
Amp Peak 2(1q43) | 7 (4%) | 184 |
0.0063 (0.466) |
0.000527 (0.0496) |
0.373 (1.00) |
0.425 (1.00) |
0.323 (1.00) |
0.171 (1.00) |
Amp Peak 4(13q31 3) | 7 (4%) | 184 |
1.96e-10 (2.2e-08) |
0.00924 (0.657) |
0.0668 (1.00) |
0.0965 (1.00) |
0.682 (1.00) |
0.2 (1.00) |
Amp Peak 5(20q11 21) | 3 (2%) | 188 |
0.00135 (0.119) |
0.101 (1.00) |
0.55 (1.00) |
|||
Del Peak 12(16q23 1) | 9 (5%) | 182 |
2.61e-07 (2.84e-05) |
0.0121 (0.798) |
0.332 (1.00) |
1 (1.00) |
0.0529 (1.00) |
0.0822 (1.00) |
Del Peak 16(20q13 13) | 4 (2%) | 187 |
9.73e-10 (1.08e-07) |
0.0302 (1.00) |
0.786 (1.00) |
1 (1.00) |
0.213 (1.00) |
0.227 (1.00) |
Del Peak 3(3q26 31) | 3 (2%) | 188 |
0.00355 (0.277) |
0.101 (1.00) |
0.786 (1.00) |
1 (1.00) |
0.0841 (1.00) |
0.094 (1.00) |
Del Peak 9(9q21 32) | 5 (3%) | 186 |
0.63 (1.00) |
0.731 (1.00) |
0.176 (1.00) |
0.664 (1.00) |
0.138 (1.00) |
0.115 (1.00) |
Del Peak 11(12q21 33) | 3 (2%) | 188 |
0.057 (1.00) |
0.529 (1.00) |
0.186 (1.00) |
0.552 (1.00) |
0.00913 (0.657) |
0.00841 (0.614) |
P value = 4.86e-07 (Chi-square test), Q value = 5.2e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
AMP PEAK 1(1P33) MUTATED | 0 | 3 | 0 | 4 | 0 |
AMP PEAK 1(1P33) WILD-TYPE | 142 | 12 | 15 | 14 | 1 |
P value = 0.000527 (Chi-square test), Q value = 0.05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 36 | 46 | 13 |
AMP PEAK 2(1Q43) MUTATED | 0 | 0 | 0 | 0 | 7 | 0 |
AMP PEAK 2(1Q43) WILD-TYPE | 46 | 18 | 26 | 36 | 39 | 13 |
P value = 4.87e-33 (Chi-square test), Q value = 5.7e-31
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
AMP PEAK 3(11Q23.3) MUTATED | 0 | 14 | 0 | 2 | 1 |
AMP PEAK 3(11Q23.3) WILD-TYPE | 142 | 1 | 15 | 16 | 0 |
P value = 0.00119 (Chi-square test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 36 | 46 | 13 |
AMP PEAK 3(11Q23.3) MUTATED | 0 | 0 | 3 | 1 | 10 | 3 |
AMP PEAK 3(11Q23.3) WILD-TYPE | 46 | 18 | 23 | 35 | 36 | 10 |
P value = 1.96e-10 (Chi-square test), Q value = 2.2e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
AMP PEAK 4(13Q31.3) MUTATED | 0 | 1 | 0 | 6 | 0 |
AMP PEAK 4(13Q31.3) WILD-TYPE | 142 | 14 | 15 | 12 | 1 |
P value = 0.00135 (Chi-square test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
AMP PEAK 5(20Q11.21) MUTATED | 0 | 0 | 2 | 1 | 0 |
AMP PEAK 5(20Q11.21) WILD-TYPE | 142 | 15 | 13 | 17 | 1 |
P value = 9.35e-32 (Chi-square test), Q value = 1.1e-29
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
AMP PEAK 6(21Q22.2) MUTATED | 0 | 0 | 13 | 1 | 0 |
AMP PEAK 6(21Q22.2) WILD-TYPE | 142 | 15 | 2 | 17 | 1 |
P value = 0.000948 (Chi-square test), Q value = 0.086
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 36 | 46 | 13 |
AMP PEAK 6(21Q22.2) MUTATED | 1 | 0 | 1 | 1 | 10 | 0 |
AMP PEAK 6(21Q22.2) WILD-TYPE | 45 | 18 | 25 | 35 | 36 | 13 |
P value = 0.00179 (Chi-square test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
DEL PEAK 2(3P13) MUTATED | 2 | 1 | 3 | 3 | 0 |
DEL PEAK 2(3P13) WILD-TYPE | 140 | 14 | 12 | 15 | 1 |
P value = 0.00258 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 38 | 57 |
DEL PEAK 2(3P13) MUTATED | 0 | 5 | 3 |
DEL PEAK 2(3P13) WILD-TYPE | 83 | 33 | 54 |
P value = 0.00208 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 37 | 79 | 62 |
DEL PEAK 2(3P13) MUTATED | 5 | 0 | 3 |
DEL PEAK 2(3P13) WILD-TYPE | 32 | 79 | 59 |
P value = 6.32e-15 (Chi-square test), Q value = 7.3e-13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
DEL PEAK 4(5Q31.2) MUTATED | 1 | 1 | 7 | 8 | 1 |
DEL PEAK 4(5Q31.2) WILD-TYPE | 141 | 14 | 8 | 10 | 0 |
P value = 5.31e-07 (Chi-square test), Q value = 5.6e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 36 | 46 | 13 |
DEL PEAK 4(5Q31.2) MUTATED | 1 | 0 | 0 | 2 | 15 | 0 |
DEL PEAK 4(5Q31.2) WILD-TYPE | 45 | 18 | 26 | 34 | 31 | 13 |
P value = 0.00131 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 38 | 57 |
DEL PEAK 4(5Q31.2) MUTATED | 4 | 10 | 3 |
DEL PEAK 4(5Q31.2) WILD-TYPE | 79 | 28 | 54 |
P value = 0.000764 (Fisher's exact test), Q value = 0.07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 37 | 79 | 62 |
DEL PEAK 4(5Q31.2) MUTATED | 10 | 3 | 4 |
DEL PEAK 4(5Q31.2) WILD-TYPE | 27 | 76 | 58 |
P value = 2.4e-07 (Chi-square test), Q value = 2.6e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
DEL PEAK 5(7P12.1) MUTATED | 7 | 1 | 0 | 7 | 1 |
DEL PEAK 5(7P12.1) WILD-TYPE | 135 | 14 | 15 | 11 | 0 |
P value = 1.06e-05 (Chi-square test), Q value = 0.0011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 36 | 46 | 13 |
DEL PEAK 5(7P12.1) MUTATED | 1 | 0 | 1 | 0 | 13 | 1 |
DEL PEAK 5(7P12.1) WILD-TYPE | 45 | 18 | 25 | 36 | 33 | 12 |
P value = 0.00179 (Fisher's exact test), Q value = 0.15
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 = 0.22
nPatients | CLUS_1 | CLUS_2 |
---|---|---|
ALL | 110 | 56 |
DEL PEAK 5(7P12.1) MUTATED | 15 | 0 |
DEL PEAK 5(7P12.1) WILD-TYPE | 95 | 56 |
P value = 8.78e-07 (Chi-square test), Q value = 9.2e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
DEL PEAK 6(7Q32.3) MUTATED | 7 | 3 | 5 | 7 | 1 |
DEL PEAK 6(7Q32.3) WILD-TYPE | 135 | 12 | 10 | 11 | 0 |
P value = 1.44e-05 (Chi-square test), Q value = 0.0015
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 36 | 46 | 13 |
DEL PEAK 6(7Q32.3) MUTATED | 1 | 1 | 2 | 1 | 16 | 2 |
DEL PEAK 6(7Q32.3) WILD-TYPE | 45 | 17 | 24 | 35 | 30 | 11 |
P value = 0.000422 (Fisher's exact test), Q value = 0.04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 38 | 57 |
DEL PEAK 6(7Q32.3) MUTATED | 4 | 12 | 6 |
DEL PEAK 6(7Q32.3) WILD-TYPE | 79 | 26 | 51 |
P value = 0.000296 (Fisher's exact test), Q value = 0.028
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 37 | 79 | 62 |
DEL PEAK 6(7Q32.3) MUTATED | 12 | 4 | 6 |
DEL PEAK 6(7Q32.3) WILD-TYPE | 25 | 75 | 56 |
P value = 2.83e-06 (Chi-square test), Q value = 0.00029
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
DEL PEAK 7(7Q34) MUTATED | 8 | 3 | 5 | 7 | 1 |
DEL PEAK 7(7Q34) WILD-TYPE | 134 | 12 | 10 | 11 | 0 |
P value = 3.61e-06 (Chi-square test), Q value = 0.00037
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 36 | 46 | 13 |
DEL PEAK 7(7Q34) MUTATED | 1 | 1 | 2 | 1 | 17 | 2 |
DEL PEAK 7(7Q34) WILD-TYPE | 45 | 17 | 24 | 35 | 29 | 11 |
P value = 9.94e-05 (Fisher's exact test), Q value = 0.0096
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 38 | 57 |
DEL PEAK 7(7Q34) MUTATED | 4 | 13 | 6 |
DEL PEAK 7(7Q34) WILD-TYPE | 79 | 25 | 51 |
P value = 8.56e-05 (Fisher's exact test), Q value = 0.0084
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 37 | 79 | 62 |
DEL PEAK 7(7Q34) MUTATED | 13 | 4 | 6 |
DEL PEAK 7(7Q34) WILD-TYPE | 24 | 75 | 56 |
P value = 8.25e-13 (Chi-square test), Q value = 9.3e-11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
DEL PEAK 10(12P13.2) MUTATED | 1 | 1 | 0 | 8 | 0 |
DEL PEAK 10(12P13.2) WILD-TYPE | 141 | 14 | 15 | 10 | 1 |
P value = 0.0022 (Chi-square test), Q value = 0.18
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 36 | 46 | 13 |
DEL PEAK 10(12P13.2) MUTATED | 0 | 0 | 0 | 1 | 8 | 1 |
DEL PEAK 10(12P13.2) WILD-TYPE | 46 | 18 | 26 | 35 | 38 | 12 |
P value = 2.61e-07 (Chi-square test), Q value = 2.8e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
DEL PEAK 12(16Q23.1) MUTATED | 2 | 1 | 1 | 4 | 1 |
DEL PEAK 12(16Q23.1) WILD-TYPE | 140 | 14 | 14 | 14 | 0 |
P value = 1.68e-14 (Chi-square test), Q value = 1.9e-12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
DEL PEAK 13(17P13.2) MUTATED | 0 | 1 | 5 | 8 | 1 |
DEL PEAK 13(17P13.2) WILD-TYPE | 142 | 14 | 10 | 10 | 0 |
P value = 2.27e-05 (Chi-square test), Q value = 0.0022
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 36 | 46 | 13 |
DEL PEAK 13(17P13.2) MUTATED | 0 | 0 | 0 | 3 | 12 | 0 |
DEL PEAK 13(17P13.2) WILD-TYPE | 46 | 18 | 26 | 33 | 34 | 13 |
P value = 0.00175 (Fisher's exact test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 37 | 79 | 62 |
DEL PEAK 13(17P13.2) MUTATED | 7 | 1 | 7 |
DEL PEAK 13(17P13.2) WILD-TYPE | 30 | 78 | 55 |
P value = 1.72e-05 (Chi-square test), Q value = 0.0017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
DEL PEAK 14(17Q11.2) MUTATED | 2 | 3 | 3 | 5 | 0 |
DEL PEAK 14(17Q11.2) WILD-TYPE | 140 | 12 | 12 | 13 | 1 |
P value = 0.00138 (Chi-square test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 36 | 46 | 13 |
DEL PEAK 14(17Q11.2) MUTATED | 0 | 0 | 0 | 4 | 9 | 0 |
DEL PEAK 14(17Q11.2) WILD-TYPE | 46 | 18 | 26 | 32 | 37 | 13 |
P value = 4.63e-07 (Chi-square test), Q value = 5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
DEL PEAK 15(18P11.21) MUTATED | 1 | 0 | 3 | 5 | 0 |
DEL PEAK 15(18P11.21) WILD-TYPE | 141 | 15 | 12 | 13 | 1 |
P value = 0.000742 (Chi-square test), Q value = 0.069
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 36 | 46 | 13 |
DEL PEAK 15(18P11.21) MUTATED | 0 | 0 | 0 | 1 | 8 | 0 |
DEL PEAK 15(18P11.21) WILD-TYPE | 46 | 18 | 26 | 35 | 38 | 13 |
P value = 9.73e-10 (Chi-square test), Q value = 1.1e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
DEL PEAK 16(20Q13.13) MUTATED | 0 | 0 | 4 | 0 | 0 |
DEL PEAK 16(20Q13.13) WILD-TYPE | 142 | 15 | 11 | 18 | 1 |
-
Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
-
Molecular subtype file = LAML-TB.transferedmergedcluster.txt
-
Number of patients = 191
-
Number of copy number variation regions = 20
-
Number of molecular subtypes = 6
-
Exclude regions that fewer than K tumors have alterations, K = 3
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 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 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.