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 10 molecular subtypes across 87 patients, 55 significant findings detected with P value < 0.05 and Q value < 0.25.
-
del_1p36.31 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
del_1p21.3 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
del_2q35 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
-
del_3p21.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_4q26 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
del_5q23.2 cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
-
del_6q22.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_6q26 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
del_10q25.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
del_11q23.2 cnv correlated to 'CN_CNMF'.
-
del_12p13.31 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CNMF'.
-
del_13q14.11 cnv correlated to 'CN_CNMF'.
-
del_14q32.31 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
-
del_15q15.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_16q24.1 cnv correlated to 'CN_CNMF'.
-
del_22q12.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE 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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
del 9p21 3 | 51 (59%) | 36 |
1e-05 (0.00035) |
0.00948 (0.0586) |
0.0252 (0.113) |
0.06 (0.213) |
0.0197 (0.0983) |
2e-05 (6e-04) |
0.962 (0.981) |
0.13 (0.325) |
0.48 (0.688) |
0.0167 (0.0857) |
del 14q32 31 | 39 (45%) | 48 |
0.00019 (0.00307) |
0.312 (0.52) |
0.524 (0.719) |
0.325 (0.537) |
0.00247 (0.0216) |
1e-05 (0.00035) |
0.027 (0.116) |
0.00923 (0.0586) |
0.042 (0.163) |
0.0798 (0.247) |
del 3p21 1 | 48 (55%) | 39 |
0.00058 (0.00754) |
0.125 (0.32) |
0.196 (0.412) |
0.598 (0.766) |
0.00016 (0.0028) |
1e-05 (0.00035) |
0.202 (0.412) |
0.0155 (0.0839) |
0.274 (0.47) |
0.00752 (0.0551) |
del 10p15 3 | 28 (32%) | 59 |
0.00175 (0.0167) |
0.00651 (0.0506) |
0.0747 (0.245) |
0.697 (0.822) |
0.0336 (0.133) |
0.0089 (0.0584) |
1 (1.00) |
0.442 (0.664) |
0.357 (0.567) |
0.448 (0.668) |
del 15q15 1 | 28 (32%) | 59 |
5e-05 (0.00131) |
0.00095 (0.0108) |
0.23 (0.443) |
0.456 (0.669) |
0.0269 (0.116) |
0.0846 (0.258) |
0.362 (0.567) |
0.525 (0.719) |
0.724 (0.831) |
0.0205 (0.1) |
del 1p36 31 | 33 (38%) | 54 |
1e-05 (0.00035) |
0.185 (0.397) |
0.468 (0.679) |
0.235 (0.444) |
0.33 (0.541) |
0.0218 (0.104) |
0.0789 (0.247) |
0.00875 (0.0584) |
0.433 (0.659) |
0.0719 (0.24) |
del 1p21 3 | 37 (43%) | 50 |
0.109 (0.289) |
0.0275 (0.116) |
0.0625 (0.215) |
0.0914 (0.267) |
0.00061 (0.00754) |
0.0156 (0.0839) |
0.926 (0.962) |
0.311 (0.52) |
0.594 (0.765) |
0.552 (0.74) |
del 4q26 | 38 (44%) | 49 |
1e-05 (0.00035) |
0.0563 (0.204) |
0.0763 (0.246) |
0.0968 (0.279) |
0.00233 (0.0213) |
0.00098 (0.0108) |
0.276 (0.47) |
0.0513 (0.192) |
0.593 (0.765) |
0.18 (0.39) |
del 4q34 3 | 41 (47%) | 46 |
1e-05 (0.00035) |
0.016 (0.0841) |
0.27 (0.468) |
0.578 (0.753) |
0.0609 (0.213) |
0.00014 (0.00267) |
0.174 (0.384) |
0.241 (0.444) |
0.961 (0.981) |
0.132 (0.326) |
del 12p13 31 | 11 (13%) | 76 |
0.115 (0.298) |
0.0129 (0.0774) |
0.0299 (0.121) |
0.561 (0.741) |
0.0232 (0.108) |
0.153 (0.356) |
0.251 (0.45) |
0.103 (0.282) |
1 (1.00) |
0.23 (0.443) |
del 22q12 2 | 68 (78%) | 19 |
0.00132 (0.0139) |
0.00011 (0.00231) |
0.531 (0.719) |
0.82 (0.898) |
0.106 (0.285) |
0.014 (0.0819) |
0.896 (0.946) |
0.627 (0.788) |
0.08 (0.247) |
0.678 (0.808) |
del 5q23 2 | 17 (20%) | 70 |
0.00022 (0.0033) |
0.378 (0.584) |
0.0029 (0.0238) |
0.257 (0.45) |
0.721 (0.831) |
0.134 (0.328) |
0.74 (0.836) |
0.437 (0.661) |
1 (1.00) |
1 (1.00) |
del 6q22 1 | 41 (47%) | 46 |
0.00155 (0.0155) |
0.245 (0.447) |
0.525 (0.719) |
0.664 (0.807) |
0.156 (0.361) |
0.496 (0.694) |
0.56 (0.741) |
0.201 (0.412) |
0.255 (0.45) |
0.0149 (0.0839) |
del 6q26 | 36 (41%) | 51 |
7e-05 (0.00163) |
0.255 (0.45) |
0.101 (0.282) |
0.166 (0.376) |
0.836 (0.899) |
0.799 (0.887) |
0.346 (0.561) |
0.492 (0.693) |
0.348 (0.561) |
0.0437 (0.167) |
del 10q25 2 | 31 (36%) | 56 |
0.00295 (0.0238) |
0.00787 (0.0551) |
0.214 (0.423) |
0.778 (0.869) |
0.485 (0.688) |
0.453 (0.669) |
0.715 (0.83) |
0.191 (0.405) |
0.233 (0.444) |
0.147 (0.348) |
del 2q35 | 17 (20%) | 70 |
0.0911 (0.267) |
0.0541 (0.199) |
0.355 (0.567) |
0.202 (0.412) |
0.553 (0.74) |
0.00761 (0.0551) |
0.482 (0.688) |
0.0858 (0.258) |
0.681 (0.808) |
0.362 (0.567) |
del 11q23 2 | 18 (21%) | 69 |
0.00049 (0.00686) |
0.716 (0.83) |
0.281 (0.475) |
0.41 (0.628) |
0.139 (0.335) |
0.216 (0.424) |
0.469 (0.679) |
0.128 (0.325) |
0.739 (0.836) |
0.11 (0.289) |
del 13q14 11 | 43 (49%) | 44 |
0.0291 (0.12) |
0.18 (0.39) |
0.572 (0.751) |
0.103 (0.282) |
0.213 (0.423) |
0.247 (0.447) |
0.962 (0.981) |
0.527 (0.719) |
0.173 (0.384) |
0.908 (0.949) |
del 16q24 1 | 22 (25%) | 65 |
0.0254 (0.113) |
0.673 (0.807) |
0.822 (0.898) |
0.665 (0.807) |
0.241 (0.444) |
0.367 (0.571) |
0.607 (0.773) |
0.164 (0.375) |
0.811 (0.896) |
0.209 (0.422) |
del 8p23 2 | 18 (21%) | 69 |
0.866 (0.922) |
0.728 (0.831) |
0.825 (0.898) |
0.901 (0.946) |
0.701 (0.822) |
0.937 (0.969) |
0.634 (0.788) |
0.833 (0.899) |
0.839 (0.899) |
0.632 (0.788) |
del 16p13 3 | 6 (7%) | 81 |
0.068 (0.23) |
0.237 (0.444) |
0.753 (0.846) |
0.672 (0.807) |
0.146 (0.348) |
0.101 (0.282) |
0.656 (0.807) |
0.658 (0.807) |
0.869 (0.922) |
0.623 (0.788) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00035
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 26 | 24 | 14 |
DEL PEAK 1(1P36.31) MUTATED | 2 | 19 | 5 | 7 |
DEL PEAK 1(1P36.31) WILD-TYPE | 21 | 7 | 19 | 7 |
P value = 0.0218 (Fisher's exact test), Q value = 0.1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 22 | 12 | 22 | 13 | 17 |
DEL PEAK 1(1P36.31) MUTATED | 3 | 8 | 11 | 5 | 6 |
DEL PEAK 1(1P36.31) WILD-TYPE | 19 | 4 | 11 | 8 | 11 |
P value = 0.00875 (Fisher's exact test), Q value = 0.058
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 29 | 25 | 6 | 13 | 14 |
DEL PEAK 1(1P36.31) MUTATED | 9 | 12 | 5 | 6 | 1 |
DEL PEAK 1(1P36.31) WILD-TYPE | 20 | 13 | 1 | 7 | 13 |
P value = 0.0275 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 14 | 20 | 26 | 27 |
DEL PEAK 2(1P21.3) MUTATED | 5 | 10 | 16 | 6 |
DEL PEAK 2(1P21.3) WILD-TYPE | 9 | 10 | 10 | 21 |
P value = 0.00061 (Fisher's exact test), Q value = 0.0075
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 26 | 22 | 17 | 21 |
DEL PEAK 2(1P21.3) MUTATED | 5 | 11 | 5 | 16 |
DEL PEAK 2(1P21.3) WILD-TYPE | 21 | 11 | 12 | 5 |
P value = 0.0156 (Fisher's exact test), Q value = 0.084
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 22 | 12 | 22 | 13 | 17 |
DEL PEAK 2(1P21.3) MUTATED | 5 | 7 | 10 | 3 | 12 |
DEL PEAK 2(1P21.3) WILD-TYPE | 17 | 5 | 12 | 10 | 5 |
P value = 0.00761 (Fisher's exact test), Q value = 0.055
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 22 | 12 | 22 | 13 | 17 |
DEL PEAK 3(2Q35) MUTATED | 1 | 6 | 7 | 1 | 2 |
DEL PEAK 3(2Q35) WILD-TYPE | 21 | 6 | 15 | 12 | 15 |
P value = 0.00058 (Fisher's exact test), Q value = 0.0075
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 26 | 24 | 14 |
DEL PEAK 4(3P21.1) MUTATED | 13 | 16 | 18 | 1 |
DEL PEAK 4(3P21.1) WILD-TYPE | 10 | 10 | 6 | 13 |
P value = 0.00016 (Fisher's exact test), Q value = 0.0028
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 26 | 22 | 17 | 21 |
DEL PEAK 4(3P21.1) MUTATED | 21 | 4 | 10 | 13 |
DEL PEAK 4(3P21.1) WILD-TYPE | 5 | 18 | 7 | 8 |
P value = 1e-05 (Fisher's exact test), Q value = 0.00035
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 22 | 12 | 22 | 13 | 17 |
DEL PEAK 4(3P21.1) MUTATED | 16 | 12 | 4 | 7 | 9 |
DEL PEAK 4(3P21.1) WILD-TYPE | 6 | 0 | 18 | 6 | 8 |
P value = 0.0155 (Fisher's exact test), Q value = 0.084
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 29 | 25 | 6 | 13 | 14 |
DEL PEAK 4(3P21.1) MUTATED | 16 | 8 | 3 | 9 | 12 |
DEL PEAK 4(3P21.1) WILD-TYPE | 13 | 17 | 3 | 4 | 2 |
P value = 0.00752 (Fisher's exact test), Q value = 0.055
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 16 | 17 | 21 | 31 |
DEL PEAK 4(3P21.1) MUTATED | 13 | 4 | 11 | 19 |
DEL PEAK 4(3P21.1) WILD-TYPE | 3 | 13 | 10 | 12 |
P value = 1e-05 (Fisher's exact test), Q value = 0.00035
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 26 | 24 | 14 |
DEL PEAK 5(4Q26) MUTATED | 3 | 21 | 6 | 8 |
DEL PEAK 5(4Q26) WILD-TYPE | 20 | 5 | 18 | 6 |
P value = 0.00233 (Fisher's exact test), Q value = 0.021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 26 | 22 | 17 | 21 |
DEL PEAK 5(4Q26) MUTATED | 4 | 11 | 9 | 14 |
DEL PEAK 5(4Q26) WILD-TYPE | 22 | 11 | 8 | 7 |
P value = 0.00098 (Fisher's exact test), Q value = 0.011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 22 | 12 | 22 | 13 | 17 |
DEL PEAK 5(4Q26) MUTATED | 2 | 8 | 12 | 5 | 11 |
DEL PEAK 5(4Q26) WILD-TYPE | 20 | 4 | 10 | 8 | 6 |
P value = 1e-05 (Fisher's exact test), Q value = 0.00035
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 26 | 24 | 14 |
DEL PEAK 6(4Q34.3) MUTATED | 3 | 22 | 7 | 9 |
DEL PEAK 6(4Q34.3) WILD-TYPE | 20 | 4 | 17 | 5 |
P value = 0.016 (Fisher's exact test), Q value = 0.084
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 14 | 20 | 26 | 27 |
DEL PEAK 6(4Q34.3) MUTATED | 4 | 15 | 13 | 9 |
DEL PEAK 6(4Q34.3) WILD-TYPE | 10 | 5 | 13 | 18 |
P value = 0.00014 (Fisher's exact test), Q value = 0.0027
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 22 | 12 | 22 | 13 | 17 |
DEL PEAK 6(4Q34.3) MUTATED | 2 | 9 | 14 | 5 | 11 |
DEL PEAK 6(4Q34.3) WILD-TYPE | 20 | 3 | 8 | 8 | 6 |
P value = 0.00022 (Fisher's exact test), Q value = 0.0033
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 26 | 24 | 14 |
DEL PEAK 7(5Q23.2) MUTATED | 0 | 10 | 7 | 0 |
DEL PEAK 7(5Q23.2) WILD-TYPE | 23 | 16 | 17 | 14 |
P value = 0.0029 (Fisher's exact test), Q value = 0.024
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 7 | 13 | 8 | 7 | 14 |
DEL PEAK 7(5Q23.2) MUTATED | 1 | 2 | 1 | 2 | 6 | 4 |
DEL PEAK 7(5Q23.2) WILD-TYPE | 13 | 5 | 12 | 6 | 1 | 10 |
P value = 0.00155 (Fisher's exact test), Q value = 0.015
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 26 | 24 | 14 |
DEL PEAK 8(6Q22.1) MUTATED | 12 | 19 | 8 | 2 |
DEL PEAK 8(6Q22.1) WILD-TYPE | 11 | 7 | 16 | 12 |
P value = 0.0149 (Fisher's exact test), Q value = 0.084
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 16 | 17 | 21 | 31 |
DEL PEAK 8(6Q22.1) MUTATED | 13 | 8 | 9 | 10 |
DEL PEAK 8(6Q22.1) WILD-TYPE | 3 | 9 | 12 | 21 |
P value = 7e-05 (Fisher's exact test), Q value = 0.0016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 26 | 24 | 14 |
DEL PEAK 9(6Q26) MUTATED | 11 | 19 | 4 | 2 |
DEL PEAK 9(6Q26) WILD-TYPE | 12 | 7 | 20 | 12 |
P value = 0.0437 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 16 | 17 | 21 | 31 |
DEL PEAK 9(6Q26) MUTATED | 11 | 9 | 6 | 10 |
DEL PEAK 9(6Q26) WILD-TYPE | 5 | 8 | 15 | 21 |
P value = 1e-05 (Fisher's exact test), Q value = 0.00035
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 26 | 24 | 14 |
DEL PEAK 11(9P21.3) MUTATED | 2 | 24 | 20 | 5 |
DEL PEAK 11(9P21.3) WILD-TYPE | 21 | 2 | 4 | 9 |
P value = 0.00948 (Fisher's exact test), Q value = 0.059
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 14 | 20 | 26 | 27 |
DEL PEAK 11(9P21.3) MUTATED | 6 | 17 | 17 | 11 |
DEL PEAK 11(9P21.3) WILD-TYPE | 8 | 3 | 9 | 16 |
P value = 0.0252 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 7 | 13 | 8 | 7 | 14 |
DEL PEAK 11(9P21.3) MUTATED | 4 | 5 | 7 | 6 | 7 | 10 |
DEL PEAK 11(9P21.3) WILD-TYPE | 10 | 2 | 6 | 2 | 0 | 4 |
P value = 0.0197 (Fisher's exact test), Q value = 0.098
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 26 | 22 | 17 | 21 |
DEL PEAK 11(9P21.3) MUTATED | 9 | 14 | 12 | 16 |
DEL PEAK 11(9P21.3) WILD-TYPE | 17 | 8 | 5 | 5 |
P value = 2e-05 (Fisher's exact test), Q value = 6e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 22 | 12 | 22 | 13 | 17 |
DEL PEAK 11(9P21.3) MUTATED | 4 | 12 | 14 | 9 | 12 |
DEL PEAK 11(9P21.3) WILD-TYPE | 18 | 0 | 8 | 4 | 5 |
P value = 0.0167 (Fisher's exact test), Q value = 0.086
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 16 | 17 | 21 | 31 |
DEL PEAK 11(9P21.3) MUTATED | 4 | 12 | 12 | 22 |
DEL PEAK 11(9P21.3) WILD-TYPE | 12 | 5 | 9 | 9 |
P value = 0.00175 (Fisher's exact test), Q value = 0.017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 26 | 24 | 14 |
DEL PEAK 12(10P15.3) MUTATED | 2 | 14 | 10 | 2 |
DEL PEAK 12(10P15.3) WILD-TYPE | 21 | 12 | 14 | 12 |
P value = 0.00651 (Fisher's exact test), Q value = 0.051
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 14 | 20 | 26 | 27 |
DEL PEAK 12(10P15.3) MUTATED | 1 | 12 | 9 | 6 |
DEL PEAK 12(10P15.3) WILD-TYPE | 13 | 8 | 17 | 21 |
P value = 0.0336 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 26 | 22 | 17 | 21 |
DEL PEAK 12(10P15.3) MUTATED | 3 | 8 | 7 | 10 |
DEL PEAK 12(10P15.3) WILD-TYPE | 23 | 14 | 10 | 11 |
P value = 0.0089 (Fisher's exact test), Q value = 0.058
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 22 | 12 | 22 | 13 | 17 |
DEL PEAK 12(10P15.3) MUTATED | 1 | 6 | 8 | 5 | 8 |
DEL PEAK 12(10P15.3) WILD-TYPE | 21 | 6 | 14 | 8 | 9 |
P value = 0.00295 (Fisher's exact test), Q value = 0.024
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 26 | 24 | 14 |
DEL PEAK 13(10Q25.2) MUTATED | 3 | 10 | 15 | 3 |
DEL PEAK 13(10Q25.2) WILD-TYPE | 20 | 16 | 9 | 11 |
P value = 0.00787 (Fisher's exact test), Q value = 0.055
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 14 | 20 | 26 | 27 |
DEL PEAK 13(10Q25.2) MUTATED | 2 | 11 | 13 | 5 |
DEL PEAK 13(10Q25.2) WILD-TYPE | 12 | 9 | 13 | 22 |
P value = 0.00049 (Fisher's exact test), Q value = 0.0069
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 26 | 24 | 14 |
DEL PEAK 14(11Q23.2) MUTATED | 0 | 3 | 10 | 5 |
DEL PEAK 14(11Q23.2) WILD-TYPE | 23 | 23 | 14 | 9 |
P value = 0.0129 (Fisher's exact test), Q value = 0.077
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 14 | 20 | 26 | 27 |
DEL PEAK 15(12P13.31) MUTATED | 1 | 7 | 2 | 1 |
DEL PEAK 15(12P13.31) WILD-TYPE | 13 | 13 | 24 | 26 |
P value = 0.0299 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 7 | 13 | 8 | 7 | 14 |
DEL PEAK 15(12P13.31) MUTATED | 0 | 1 | 0 | 3 | 1 | 4 |
DEL PEAK 15(12P13.31) WILD-TYPE | 14 | 6 | 13 | 5 | 6 | 10 |
P value = 0.0232 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 26 | 22 | 17 | 21 |
DEL PEAK 15(12P13.31) MUTATED | 0 | 5 | 4 | 2 |
DEL PEAK 15(12P13.31) WILD-TYPE | 26 | 17 | 13 | 19 |
P value = 0.0291 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 26 | 24 | 14 |
DEL PEAK 16(13Q14.11) MUTATED | 8 | 19 | 11 | 5 |
DEL PEAK 16(13Q14.11) WILD-TYPE | 15 | 7 | 13 | 9 |
P value = 0.00019 (Fisher's exact test), Q value = 0.0031
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 26 | 24 | 14 |
DEL PEAK 17(14Q32.31) MUTATED | 4 | 18 | 7 | 10 |
DEL PEAK 17(14Q32.31) WILD-TYPE | 19 | 8 | 17 | 4 |
P value = 0.00247 (Fisher's exact test), Q value = 0.022
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 26 | 22 | 17 | 21 |
DEL PEAK 17(14Q32.31) MUTATED | 7 | 17 | 5 | 10 |
DEL PEAK 17(14Q32.31) WILD-TYPE | 19 | 5 | 12 | 11 |
P value = 1e-05 (Fisher's exact test), Q value = 0.00035
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 22 | 12 | 22 | 13 | 17 |
DEL PEAK 17(14Q32.31) MUTATED | 4 | 9 | 18 | 1 | 7 |
DEL PEAK 17(14Q32.31) WILD-TYPE | 18 | 3 | 4 | 12 | 10 |
P value = 0.027 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 36 | 29 | 22 |
DEL PEAK 17(14Q32.31) MUTATED | 10 | 16 | 13 |
DEL PEAK 17(14Q32.31) WILD-TYPE | 26 | 13 | 9 |
P value = 0.00923 (Fisher's exact test), Q value = 0.059
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 29 | 25 | 6 | 13 | 14 |
DEL PEAK 17(14Q32.31) MUTATED | 8 | 15 | 4 | 9 | 3 |
DEL PEAK 17(14Q32.31) WILD-TYPE | 21 | 10 | 2 | 4 | 11 |
P value = 0.042 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 37 | 27 | 21 |
DEL PEAK 17(14Q32.31) MUTATED | 21 | 7 | 10 |
DEL PEAK 17(14Q32.31) WILD-TYPE | 16 | 20 | 11 |
P value = 5e-05 (Fisher's exact test), Q value = 0.0013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 26 | 24 | 14 |
DEL PEAK 18(15Q15.1) MUTATED | 0 | 9 | 15 | 4 |
DEL PEAK 18(15Q15.1) WILD-TYPE | 23 | 17 | 9 | 10 |
P value = 0.00095 (Fisher's exact test), Q value = 0.011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 14 | 20 | 26 | 27 |
DEL PEAK 18(15Q15.1) MUTATED | 1 | 12 | 11 | 4 |
DEL PEAK 18(15Q15.1) WILD-TYPE | 13 | 8 | 15 | 23 |
P value = 0.0269 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 26 | 22 | 17 | 21 |
DEL PEAK 18(15Q15.1) MUTATED | 3 | 11 | 6 | 8 |
DEL PEAK 18(15Q15.1) WILD-TYPE | 23 | 11 | 11 | 13 |
P value = 0.0205 (Fisher's exact test), Q value = 0.1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 16 | 17 | 21 | 31 |
DEL PEAK 18(15Q15.1) MUTATED | 3 | 8 | 2 | 13 |
DEL PEAK 18(15Q15.1) WILD-TYPE | 13 | 9 | 19 | 18 |
P value = 0.0254 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 26 | 24 | 14 |
DEL PEAK 20(16Q24.1) MUTATED | 1 | 7 | 9 | 5 |
DEL PEAK 20(16Q24.1) WILD-TYPE | 22 | 19 | 15 | 9 |
P value = 0.00132 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 26 | 24 | 14 |
DEL PEAK 21(22Q12.2) MUTATED | 12 | 23 | 23 | 10 |
DEL PEAK 21(22Q12.2) WILD-TYPE | 11 | 3 | 1 | 4 |
P value = 0.00011 (Fisher's exact test), Q value = 0.0023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 14 | 20 | 26 | 27 |
DEL PEAK 21(22Q12.2) MUTATED | 10 | 19 | 25 | 14 |
DEL PEAK 21(22Q12.2) WILD-TYPE | 4 | 1 | 1 | 13 |
P value = 0.014 (Fisher's exact test), Q value = 0.082
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 22 | 12 | 22 | 13 | 17 |
DEL PEAK 21(22Q12.2) MUTATED | 15 | 12 | 18 | 7 | 16 |
DEL PEAK 21(22Q12.2) WILD-TYPE | 7 | 0 | 4 | 6 | 1 |
-
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/MESO-TP/19781625/transformed.cor.cli.txt
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Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/MESO-TP/20139528/MESO-TP.transferedmergedcluster.txt
-
Number of patients = 87
-
Number of significantly focal cnvs = 21
-
Number of molecular subtypes = 10
-
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.