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, 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_7q32.3 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'.
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 (0.00122) |
5e-05 (0.00555) |
0.00545 (0.447) |
0.00064 (0.064) |
0.00088 (0.0854) |
0.00144 (0.135) |
del 7q32 3 | 23 (12%) | 168 |
1e-05 (0.00122) |
0.00014 (0.0148) |
0.0387 (1.00) |
2e-05 (0.00228) |
0.00287 (0.25) |
0.00208 (0.185) |
del 7q34 | 24 (13%) | 167 |
1e-05 (0.00122) |
5e-05 (0.00555) |
0.0217 (1.00) |
1e-05 (0.00122) |
0.00083 (0.0813) |
0.00059 (0.0596) |
del 7p12 1 | 16 (8%) | 175 |
0.00027 (0.0281) |
0.00064 (0.064) |
0.00155 (0.143) |
2e-05 (0.00228) |
0.00599 (0.485) |
0.00666 (0.526) |
del 17p13 2 | 15 (8%) | 176 |
1e-05 (0.00122) |
0.00095 (0.0912) |
0.0112 (0.806) |
0.00033 (0.034) |
0.0871 (1.00) |
0.00133 (0.126) |
amp 21q22 2 | 14 (7%) | 177 |
1e-05 (0.00122) |
0.00224 (0.197) |
0.00318 (0.273) |
0.0375 (1.00) |
0.00147 (0.137) |
0.0674 (1.00) |
amp 11q23 3 | 17 (9%) | 174 |
1e-05 (0.00122) |
7e-05 (0.00763) |
0.373 (1.00) |
0.203 (1.00) |
0.747 (1.00) |
0.186 (1.00) |
amp 1p33 | 7 (4%) | 184 |
0.00056 (0.0571) |
0.0125 (0.848) |
0.125 (1.00) |
0.13 (1.00) |
0.00931 (0.689) |
0.0475 (1.00) |
amp 19p13 2 | 6 (3%) | 185 |
0.00013 (0.0139) |
0.556 (1.00) |
0.858 (1.00) |
0.629 (1.00) |
0.894 (1.00) |
1 (1.00) |
del 3p13 | 9 (5%) | 182 |
0.00014 (0.0148) |
0.298 (1.00) |
0.0338 (1.00) |
0.127 (1.00) |
0.012 (0.839) |
0.0196 (1.00) |
del 12p13 2 | 10 (5%) | 181 |
8e-05 (0.00864) |
0.00482 (0.4) |
0.199 (1.00) |
0.0738 (1.00) |
0.0678 (1.00) |
0.00972 (0.71) |
del 12q21 33 | 3 (2%) | 188 |
0.00173 (0.157) |
0.303 (1.00) |
0.187 (1.00) |
0.59 (1.00) |
0.00783 (0.603) |
0.00668 (0.526) |
del 16q23 1 | 9 (5%) | 182 |
0.00179 (0.161) |
0.149 (1.00) |
0.332 (1.00) |
0.495 (1.00) |
0.0456 (1.00) |
0.0631 (1.00) |
del 17q11 2 | 13 (7%) | 178 |
2e-05 (0.00228) |
0.0214 (1.00) |
0.155 (1.00) |
0.00653 (0.522) |
0.136 (1.00) |
0.00365 (0.31) |
del 18p11 21 | 9 (5%) | 182 |
1e-05 (0.00122) |
0.0183 (1.00) |
0.382 (1.00) |
0.336 (1.00) |
0.211 (1.00) |
0.0334 (1.00) |
amp 1q43 | 7 (4%) | 184 |
0.00458 (0.385) |
0.0118 (0.839) |
0.374 (1.00) |
0.0355 (1.00) |
0.138 (1.00) |
0.0153 (1.00) |
amp 13q31 3 | 7 (4%) | 184 |
0.0841 (1.00) |
0.0119 (0.839) |
0.0682 (1.00) |
0.0364 (1.00) |
0.734 (1.00) |
0.0562 (1.00) |
amp 20q11 21 | 3 (2%) | 188 |
0.00792 (0.603) |
0.267 (1.00) |
||||
del 3q26 31 | 3 (2%) | 188 |
0.00835 (0.626) |
0.268 (1.00) |
0.786 (1.00) |
1 (1.00) |
0.0612 (1.00) |
0.0925 (1.00) |
del 9q21 32 | 5 (3%) | 186 |
0.252 (1.00) |
0.516 (1.00) |
0.176 (1.00) |
0.603 (1.00) |
0.184 (1.00) |
0.105 (1.00) |
del 20q13 13 | 4 (2%) | 187 |
0.0255 (1.00) |
0.146 (1.00) |
0.786 (1.00) |
0.586 (1.00) |
0.123 (1.00) |
0.413 (1.00) |
P value = 0.00056 (Fisher's exact test), Q value = 0.057
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 = 1e-05 (Fisher's exact test), Q value = 0.0012
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 = 7e-05 (Fisher's exact test), Q value = 0.0076
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 = 0.00013 (Fisher's exact test), Q value = 0.014
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 = 1e-05 (Fisher's exact test), Q value = 0.0012
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 = 0.00224 (Fisher's exact test), Q value = 0.2
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 = 0.00147 (Fisher's exact test), Q value = 0.14
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 = 0.00014 (Fisher's exact test), Q value = 0.015
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 = 1e-05 (Fisher's exact test), Q value = 0.0012
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 = 5e-05 (Fisher's exact test), Q value = 0.0055
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 = 0.00064 (Fisher's exact test), Q value = 0.064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 16 | 13 | 14 | 55 | 26 | 42 |
DEL PEAK 4(5Q31.2) MUTATED | 0 | 0 | 0 | 14 | 0 | 2 |
DEL PEAK 4(5Q31.2) WILD-TYPE | 16 | 13 | 14 | 41 | 26 | 40 |
P value = 0.00088 (Fisher's exact test), Q value = 0.085
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 = 0.00144 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 34 | 78 |
DEL PEAK 4(5Q31.2) MUTATED | 1 | 8 | 8 |
DEL PEAK 4(5Q31.2) WILD-TYPE | 66 | 26 | 70 |
P value = 0.00027 (Fisher's exact test), Q value = 0.028
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 = 0.00064 (Fisher's exact test), Q value = 0.064
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 = 0.00155 (Fisher's exact test), Q value = 0.14
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 = 2e-05 (Fisher's exact test), Q value = 0.0023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 16 | 13 | 14 | 55 | 26 | 42 |
DEL PEAK 5(7P12.1) MUTATED | 0 | 0 | 0 | 15 | 0 | 0 |
DEL PEAK 5(7P12.1) WILD-TYPE | 16 | 13 | 14 | 40 | 26 | 42 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0012
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 = 0.00014 (Fisher's exact test), Q value = 0.015
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 = 2e-05 (Fisher's exact test), Q value = 0.0023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 16 | 13 | 14 | 55 | 26 | 42 |
DEL PEAK 6(7Q32.3) MUTATED | 1 | 1 | 0 | 17 | 0 | 0 |
DEL PEAK 6(7Q32.3) WILD-TYPE | 15 | 12 | 14 | 38 | 26 | 42 |
P value = 0.00287 (Fisher's exact test), Q value = 0.25
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 37 | 41 | 43 |
DEL PEAK 6(7Q32.3) MUTATED | 2 | 11 | 5 | 4 |
DEL PEAK 6(7Q32.3) WILD-TYPE | 56 | 26 | 36 | 39 |
P value = 0.00208 (Fisher's exact test), Q value = 0.19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 34 | 78 |
DEL PEAK 6(7Q32.3) MUTATED | 2 | 9 | 11 |
DEL PEAK 6(7Q32.3) WILD-TYPE | 65 | 25 | 67 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0012
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 = 5e-05 (Fisher's exact test), Q value = 0.0055
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 = 1e-05 (Fisher's exact test), Q value = 0.0012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 16 | 13 | 14 | 55 | 26 | 42 |
DEL PEAK 7(7Q34) MUTATED | 1 | 1 | 0 | 18 | 0 | 0 |
DEL PEAK 7(7Q34) WILD-TYPE | 15 | 12 | 14 | 37 | 26 | 42 |
P value = 0.00083 (Fisher's exact test), Q value = 0.081
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 = 0.00059 (Fisher's exact test), Q value = 0.06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 34 | 78 |
DEL PEAK 7(7Q34) MUTATED | 2 | 10 | 11 |
DEL PEAK 7(7Q34) WILD-TYPE | 65 | 24 | 67 |
P value = 8e-05 (Fisher's exact test), Q value = 0.0086
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 = 0.00173 (Fisher's exact test), Q value = 0.16
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 = 0.00179 (Fisher's exact test), Q value = 0.16
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 = 1e-05 (Fisher's exact test), Q value = 0.0012
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 = 0.00095 (Fisher's exact test), Q value = 0.091
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 = 0.00033 (Fisher's exact test), Q value = 0.034
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 |
P value = 0.00133 (Fisher's exact test), Q value = 0.13
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 |
P value = 2e-05 (Fisher's exact test), Q value = 0.0023
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 = 1e-05 (Fisher's exact test), Q value = 0.0012
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 |
-
Copy number data file = transformed.cor.cli.txt
-
Molecular subtype file = LAML-TB.transferedmergedcluster.txt
-
Number of patients = 191
-
Number of significantly focal cnvs = 21
-
Number of molecular subtypes = 6
-
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 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.