This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 12 focal events and 10 molecular subtypes across 123 patients, 69 significant findings detected with P value < 0.05 and Q value < 0.25.
-
del_2q37.1 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
del_3p22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_6p25.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_6q21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_7q36.3 cnv correlated to 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_9q22.33 cnv correlated to 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
del_10q26.3 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_11q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_19p13.11 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
del_22q12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CNMF'.
-
del_22q13.32 cnv correlated to 'CN_CNMF', 'RPPA_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 6p25 2 | 26 (21%) | 97 |
1e-05 (1e-04) |
1e-05 (1e-04) |
2e-05 (0.000141) |
0.00023 (0.00106) |
0.00173 (0.00649) |
4e-05 (0.00024) |
0.0012 (0.0048) |
0.00654 (0.0196) |
2e-05 (0.000141) |
0.00491 (0.0155) |
del 6q21 | 20 (16%) | 103 |
1e-05 (1e-04) |
1e-05 (1e-04) |
1e-05 (1e-04) |
3e-05 (0.000189) |
1e-05 (1e-04) |
1e-05 (1e-04) |
2e-05 (0.000141) |
0.00021 (0.00101) |
1e-05 (1e-04) |
2e-05 (0.000141) |
del 3p22 2 | 14 (11%) | 109 |
6e-05 (0.000327) |
1e-05 (1e-04) |
0.00669 (0.0196) |
1e-05 (1e-04) |
0.0324 (0.0647) |
0.0152 (0.0379) |
0.0245 (0.0564) |
0.0656 (0.104) |
0.00055 (0.00236) |
0.0296 (0.0635) |
del 11q22 1 | 7 (6%) | 116 |
9e-05 (0.00047) |
2e-05 (0.000141) |
0.0281 (0.0625) |
0.00598 (0.0184) |
0.0317 (0.0647) |
0.0138 (0.0369) |
0.0337 (0.0653) |
0.114 (0.159) |
0.00217 (0.00766) |
0.00873 (0.0249) |
del 9p21 3 | 11 (9%) | 112 |
0.0158 (0.0379) |
0.00366 (0.0125) |
0.0795 (0.119) |
0.00129 (0.00499) |
5e-05 (0.000286) |
1e-05 (1e-04) |
0.558 (0.62) |
0.00019 (0.00095) |
0.143 (0.196) |
0.0157 (0.0379) |
del 9q22 33 | 3 (2%) | 120 |
0.603 (0.658) |
0.177 (0.23) |
0.0421 (0.0778) |
0.0145 (0.0379) |
0.0495 (0.0861) |
0.0294 (0.0635) |
0.197 (0.25) |
0.0667 (0.104) |
0.106 (0.152) |
0.0582 (0.0983) |
del 19p13 11 | 5 (4%) | 118 |
0.259 (0.308) |
0.0441 (0.0798) |
0.177 (0.23) |
0.203 (0.251) |
0.00202 (0.00735) |
0.00035 (0.00156) |
0.724 (0.755) |
0.00487 (0.0155) |
0.574 (0.632) |
0.172 (0.229) |
del 22q12 1 | 19 (15%) | 104 |
1e-05 (1e-04) |
0.0136 (0.0369) |
0.0133 (0.0369) |
0.0556 (0.0953) |
0.0155 (0.0379) |
0.0731 (0.112) |
0.245 (0.294) |
0.456 (0.516) |
0.522 (0.585) |
0.429 (0.49) |
del 2q37 1 | 5 (4%) | 118 |
0.262 (0.308) |
0.0446 (0.0798) |
0.0329 (0.0647) |
0.112 (0.159) |
0.629 (0.668) |
0.307 (0.354) |
1 (1.00) |
0.0201 (0.0473) |
1 (1.00) |
0.169 (0.227) |
del 7q36 3 | 3 (2%) | 120 |
0.0597 (0.0995) |
0.178 (0.23) |
0.0421 (0.0778) |
0.202 (0.251) |
0.00115 (0.00476) |
0.00391 (0.013) |
0.648 (0.682) |
0.117 (0.162) |
0.106 (0.152) |
0.617 (0.667) |
del 10q26 3 | 6 (5%) | 117 |
0.625 (0.668) |
0.0388 (0.0739) |
0.0917 (0.134) |
0.0319 (0.0647) |
0.0659 (0.104) |
0.223 (0.27) |
0.739 (0.765) |
0.0666 (0.104) |
0.856 (0.878) |
0.0488 (0.0861) |
del 22q13 32 | 15 (12%) | 108 |
3e-05 (0.000189) |
0.0852 (0.126) |
0.0304 (0.064) |
0.0793 (0.119) |
0.0648 (0.104) |
0.0249 (0.0564) |
0.207 (0.254) |
0.297 (0.347) |
0.198 (0.25) |
0.898 (0.914) |
P value = 0.0446 (Fisher's exact test), Q value = 0.08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 36 | 24 | 24 |
DEL PEAK 1(2Q37.1) MUTATED | 0 | 4 | 1 | 0 |
DEL PEAK 1(2Q37.1) WILD-TYPE | 39 | 32 | 23 | 24 |
P value = 0.0329 (Fisher's exact test), Q value = 0.065
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 24 | 39 |
DEL PEAK 1(2Q37.1) MUTATED | 1 | 3 | 0 |
DEL PEAK 1(2Q37.1) WILD-TYPE | 26 | 21 | 39 |
P value = 0.0201 (Fisher's exact test), Q value = 0.047
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 27 | 18 | 28 | 7 | 16 | 27 |
DEL PEAK 1(2Q37.1) MUTATED | 0 | 3 | 1 | 1 | 0 | 0 |
DEL PEAK 1(2Q37.1) WILD-TYPE | 27 | 15 | 27 | 6 | 16 | 27 |
P value = 6e-05 (Fisher's exact test), Q value = 0.00033
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 31 | 27 |
DEL PEAK 2(3P22.2) MUTATED | 1 | 10 | 3 |
DEL PEAK 2(3P22.2) WILD-TYPE | 64 | 21 | 24 |
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 36 | 24 | 24 |
DEL PEAK 2(3P22.2) MUTATED | 0 | 3 | 10 | 1 |
DEL PEAK 2(3P22.2) WILD-TYPE | 39 | 33 | 14 | 23 |
P value = 0.00669 (Fisher's exact test), Q value = 0.02
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 24 | 39 |
DEL PEAK 2(3P22.2) MUTATED | 8 | 1 | 2 |
DEL PEAK 2(3P22.2) WILD-TYPE | 19 | 23 | 37 |
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 16 | 23 | 31 | 20 |
DEL PEAK 2(3P22.2) MUTATED | 3 | 0 | 0 | 8 |
DEL PEAK 2(3P22.2) WILD-TYPE | 13 | 23 | 31 | 12 |
P value = 0.0324 (Fisher's exact test), Q value = 0.065
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 31 | 29 | 14 |
DEL PEAK 2(3P22.2) MUTATED | 9 | 1 | 1 | 3 |
DEL PEAK 2(3P22.2) WILD-TYPE | 36 | 30 | 28 | 11 |
P value = 0.0152 (Fisher's exact test), Q value = 0.038
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 42 | 20 | 10 |
DEL PEAK 2(3P22.2) MUTATED | 10 | 1 | 1 | 2 |
DEL PEAK 2(3P22.2) WILD-TYPE | 37 | 41 | 19 | 8 |
P value = 0.0245 (Fisher's exact test), Q value = 0.056
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 58 | 61 | 1 | 2 | 1 |
DEL PEAK 2(3P22.2) MUTATED | 12 | 2 | 0 | 0 | 0 |
DEL PEAK 2(3P22.2) WILD-TYPE | 46 | 59 | 1 | 2 | 1 |
P value = 0.00055 (Fisher's exact test), Q value = 0.0024
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 59 | 46 |
DEL PEAK 2(3P22.2) MUTATED | 0 | 2 | 12 |
DEL PEAK 2(3P22.2) WILD-TYPE | 18 | 57 | 34 |
P value = 0.0296 (Fisher's exact test), Q value = 0.064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 29 | 33 | 33 | 28 |
DEL PEAK 2(3P22.2) MUTATED | 7 | 1 | 5 | 1 |
DEL PEAK 2(3P22.2) WILD-TYPE | 22 | 32 | 28 | 27 |
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 31 | 27 |
DEL PEAK 3(6P25.2) MUTATED | 1 | 20 | 5 |
DEL PEAK 3(6P25.2) WILD-TYPE | 64 | 11 | 22 |
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 36 | 24 | 24 |
DEL PEAK 3(6P25.2) MUTATED | 2 | 6 | 15 | 3 |
DEL PEAK 3(6P25.2) WILD-TYPE | 37 | 30 | 9 | 21 |
P value = 2e-05 (Fisher's exact test), Q value = 0.00014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 24 | 39 |
DEL PEAK 3(6P25.2) MUTATED | 15 | 4 | 2 |
DEL PEAK 3(6P25.2) WILD-TYPE | 12 | 20 | 37 |
P value = 0.00023 (Fisher's exact test), Q value = 0.0011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 16 | 23 | 31 | 20 |
DEL PEAK 3(6P25.2) MUTATED | 3 | 4 | 2 | 12 |
DEL PEAK 3(6P25.2) WILD-TYPE | 13 | 19 | 29 | 8 |
P value = 0.00173 (Fisher's exact test), Q value = 0.0065
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 31 | 29 | 14 |
DEL PEAK 3(6P25.2) MUTATED | 14 | 1 | 4 | 6 |
DEL PEAK 3(6P25.2) WILD-TYPE | 31 | 30 | 25 | 8 |
P value = 4e-05 (Fisher's exact test), Q value = 0.00024
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 42 | 20 | 10 |
DEL PEAK 3(6P25.2) MUTATED | 15 | 4 | 0 | 6 |
DEL PEAK 3(6P25.2) WILD-TYPE | 32 | 38 | 20 | 4 |
P value = 0.0012 (Fisher's exact test), Q value = 0.0048
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 58 | 61 | 1 | 2 | 1 |
DEL PEAK 3(6P25.2) MUTATED | 20 | 5 | 0 | 1 | 0 |
DEL PEAK 3(6P25.2) WILD-TYPE | 38 | 56 | 1 | 1 | 1 |
P value = 0.00654 (Fisher's exact test), Q value = 0.02
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 27 | 18 | 28 | 7 | 16 | 27 |
DEL PEAK 3(6P25.2) MUTATED | 10 | 3 | 8 | 3 | 0 | 2 |
DEL PEAK 3(6P25.2) WILD-TYPE | 17 | 15 | 20 | 4 | 16 | 25 |
P value = 2e-05 (Fisher's exact test), Q value = 0.00014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 59 | 46 |
DEL PEAK 3(6P25.2) MUTATED | 1 | 5 | 20 |
DEL PEAK 3(6P25.2) WILD-TYPE | 17 | 54 | 26 |
P value = 0.00491 (Fisher's exact test), Q value = 0.016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 29 | 33 | 33 | 28 |
DEL PEAK 3(6P25.2) MUTATED | 11 | 3 | 10 | 2 |
DEL PEAK 3(6P25.2) WILD-TYPE | 18 | 30 | 23 | 26 |
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 31 | 27 |
DEL PEAK 4(6Q21) MUTATED | 0 | 18 | 2 |
DEL PEAK 4(6Q21) WILD-TYPE | 65 | 13 | 25 |
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 36 | 24 | 24 |
DEL PEAK 4(6Q21) MUTATED | 1 | 3 | 16 | 0 |
DEL PEAK 4(6Q21) WILD-TYPE | 38 | 33 | 8 | 24 |
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 24 | 39 |
DEL PEAK 4(6Q21) MUTATED | 13 | 1 | 1 |
DEL PEAK 4(6Q21) WILD-TYPE | 14 | 23 | 38 |
P value = 3e-05 (Fisher's exact test), Q value = 0.00019
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 16 | 23 | 31 | 20 |
DEL PEAK 4(6Q21) MUTATED | 2 | 1 | 1 | 11 |
DEL PEAK 4(6Q21) WILD-TYPE | 14 | 22 | 30 | 9 |
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 31 | 29 | 14 |
DEL PEAK 4(6Q21) MUTATED | 13 | 0 | 0 | 7 |
DEL PEAK 4(6Q21) WILD-TYPE | 32 | 31 | 29 | 7 |
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 42 | 20 | 10 |
DEL PEAK 4(6Q21) MUTATED | 14 | 0 | 1 | 5 |
DEL PEAK 4(6Q21) WILD-TYPE | 33 | 42 | 19 | 5 |
P value = 2e-05 (Fisher's exact test), Q value = 0.00014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 58 | 61 | 1 | 2 | 1 |
DEL PEAK 4(6Q21) MUTATED | 18 | 1 | 0 | 1 | 0 |
DEL PEAK 4(6Q21) WILD-TYPE | 40 | 60 | 1 | 1 | 1 |
P value = 0.00021 (Fisher's exact test), Q value = 0.001
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 27 | 18 | 28 | 7 | 16 | 27 |
DEL PEAK 4(6Q21) MUTATED | 9 | 0 | 7 | 3 | 1 | 0 |
DEL PEAK 4(6Q21) WILD-TYPE | 18 | 18 | 21 | 4 | 15 | 27 |
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 59 | 46 |
DEL PEAK 4(6Q21) MUTATED | 0 | 0 | 20 |
DEL PEAK 4(6Q21) WILD-TYPE | 18 | 59 | 26 |
P value = 2e-05 (Fisher's exact test), Q value = 0.00014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 29 | 33 | 33 | 28 |
DEL PEAK 4(6Q21) MUTATED | 10 | 1 | 9 | 0 |
DEL PEAK 4(6Q21) WILD-TYPE | 19 | 32 | 24 | 28 |
P value = 0.0421 (Fisher's exact test), Q value = 0.078
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 24 | 39 |
DEL PEAK 5(7Q36.3) MUTATED | 3 | 0 | 0 |
DEL PEAK 5(7Q36.3) WILD-TYPE | 24 | 24 | 39 |
P value = 0.00115 (Fisher's exact test), Q value = 0.0048
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 31 | 29 | 14 |
DEL PEAK 5(7Q36.3) MUTATED | 0 | 0 | 0 | 3 |
DEL PEAK 5(7Q36.3) WILD-TYPE | 45 | 31 | 29 | 11 |
P value = 0.00391 (Fisher's exact test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 42 | 20 | 10 |
DEL PEAK 5(7Q36.3) MUTATED | 0 | 0 | 1 | 2 |
DEL PEAK 5(7Q36.3) WILD-TYPE | 47 | 42 | 19 | 8 |
P value = 0.0158 (Fisher's exact test), Q value = 0.038
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 31 | 27 |
DEL PEAK 6(9P21.3) MUTATED | 2 | 6 | 3 |
DEL PEAK 6(9P21.3) WILD-TYPE | 63 | 25 | 24 |
P value = 0.00366 (Fisher's exact test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 36 | 24 | 24 |
DEL PEAK 6(9P21.3) MUTATED | 0 | 8 | 2 | 1 |
DEL PEAK 6(9P21.3) WILD-TYPE | 39 | 28 | 22 | 23 |
P value = 0.00129 (Fisher's exact test), Q value = 0.005
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 16 | 23 | 31 | 20 |
DEL PEAK 6(9P21.3) MUTATED | 0 | 3 | 0 | 6 |
DEL PEAK 6(9P21.3) WILD-TYPE | 16 | 20 | 31 | 14 |
P value = 5e-05 (Fisher's exact test), Q value = 0.00029
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 31 | 29 | 14 |
DEL PEAK 6(9P21.3) MUTATED | 1 | 0 | 3 | 6 |
DEL PEAK 6(9P21.3) WILD-TYPE | 44 | 31 | 26 | 8 |
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 42 | 20 | 10 |
DEL PEAK 6(9P21.3) MUTATED | 1 | 0 | 3 | 6 |
DEL PEAK 6(9P21.3) WILD-TYPE | 46 | 42 | 17 | 4 |
P value = 0.00019 (Fisher's exact test), Q value = 0.00095
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 27 | 18 | 28 | 7 | 16 | 27 |
DEL PEAK 6(9P21.3) MUTATED | 0 | 0 | 3 | 4 | 3 | 1 |
DEL PEAK 6(9P21.3) WILD-TYPE | 27 | 18 | 25 | 3 | 13 | 26 |
P value = 0.0157 (Fisher's exact test), Q value = 0.038
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 29 | 33 | 33 | 28 |
DEL PEAK 6(9P21.3) MUTATED | 0 | 3 | 7 | 1 |
DEL PEAK 6(9P21.3) WILD-TYPE | 29 | 30 | 26 | 27 |
P value = 0.0421 (Fisher's exact test), Q value = 0.078
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 24 | 39 |
DEL PEAK 7(9Q22.33) MUTATED | 3 | 0 | 0 |
DEL PEAK 7(9Q22.33) WILD-TYPE | 24 | 24 | 39 |
P value = 0.0145 (Fisher's exact test), Q value = 0.038
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 16 | 23 | 31 | 20 |
DEL PEAK 7(9Q22.33) MUTATED | 0 | 0 | 0 | 3 |
DEL PEAK 7(9Q22.33) WILD-TYPE | 16 | 23 | 31 | 17 |
P value = 0.0495 (Fisher's exact test), Q value = 0.086
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 31 | 29 | 14 |
DEL PEAK 7(9Q22.33) MUTATED | 1 | 0 | 0 | 2 |
DEL PEAK 7(9Q22.33) WILD-TYPE | 44 | 31 | 29 | 12 |
P value = 0.0294 (Fisher's exact test), Q value = 0.064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 42 | 20 | 10 |
DEL PEAK 7(9Q22.33) MUTATED | 1 | 0 | 0 | 2 |
DEL PEAK 7(9Q22.33) WILD-TYPE | 46 | 42 | 20 | 8 |
P value = 0.0388 (Fisher's exact test), Q value = 0.074
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 36 | 24 | 24 |
DEL PEAK 8(10Q26.3) MUTATED | 0 | 3 | 3 | 0 |
DEL PEAK 8(10Q26.3) WILD-TYPE | 39 | 33 | 21 | 24 |
P value = 0.0319 (Fisher's exact test), Q value = 0.065
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 16 | 23 | 31 | 20 |
DEL PEAK 8(10Q26.3) MUTATED | 0 | 4 | 0 | 1 |
DEL PEAK 8(10Q26.3) WILD-TYPE | 16 | 19 | 31 | 19 |
P value = 0.0488 (Fisher's exact test), Q value = 0.086
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 29 | 33 | 33 | 28 |
DEL PEAK 8(10Q26.3) MUTATED | 2 | 4 | 0 | 0 |
DEL PEAK 8(10Q26.3) WILD-TYPE | 27 | 29 | 33 | 28 |
P value = 9e-05 (Fisher's exact test), Q value = 0.00047
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 31 | 27 |
DEL PEAK 9(11Q22.1) MUTATED | 0 | 7 | 0 |
DEL PEAK 9(11Q22.1) WILD-TYPE | 65 | 24 | 27 |
P value = 2e-05 (Fisher's exact test), Q value = 0.00014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 36 | 24 | 24 |
DEL PEAK 9(11Q22.1) MUTATED | 0 | 0 | 7 | 0 |
DEL PEAK 9(11Q22.1) WILD-TYPE | 39 | 36 | 17 | 24 |
P value = 0.0281 (Fisher's exact test), Q value = 0.062
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 24 | 39 |
DEL PEAK 9(11Q22.1) MUTATED | 4 | 1 | 0 |
DEL PEAK 9(11Q22.1) WILD-TYPE | 23 | 23 | 39 |
P value = 0.00598 (Fisher's exact test), Q value = 0.018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 16 | 23 | 31 | 20 |
DEL PEAK 9(11Q22.1) MUTATED | 1 | 0 | 0 | 4 |
DEL PEAK 9(11Q22.1) WILD-TYPE | 15 | 23 | 31 | 16 |
P value = 0.0317 (Fisher's exact test), Q value = 0.065
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 31 | 29 | 14 |
DEL PEAK 9(11Q22.1) MUTATED | 6 | 0 | 0 | 1 |
DEL PEAK 9(11Q22.1) WILD-TYPE | 39 | 31 | 29 | 13 |
P value = 0.0138 (Fisher's exact test), Q value = 0.037
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 42 | 20 | 10 |
DEL PEAK 9(11Q22.1) MUTATED | 7 | 0 | 0 | 0 |
DEL PEAK 9(11Q22.1) WILD-TYPE | 40 | 42 | 20 | 10 |
P value = 0.0337 (Fisher's exact test), Q value = 0.065
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 58 | 61 | 1 | 2 | 1 |
DEL PEAK 9(11Q22.1) MUTATED | 7 | 0 | 0 | 0 | 0 |
DEL PEAK 9(11Q22.1) WILD-TYPE | 51 | 61 | 1 | 2 | 1 |
P value = 0.00217 (Fisher's exact test), Q value = 0.0077
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 59 | 46 |
DEL PEAK 9(11Q22.1) MUTATED | 0 | 0 | 7 |
DEL PEAK 9(11Q22.1) WILD-TYPE | 18 | 59 | 39 |
P value = 0.00873 (Fisher's exact test), Q value = 0.025
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 29 | 33 | 33 | 28 |
DEL PEAK 9(11Q22.1) MUTATED | 5 | 0 | 2 | 0 |
DEL PEAK 9(11Q22.1) WILD-TYPE | 24 | 33 | 31 | 28 |
P value = 0.0441 (Fisher's exact test), Q value = 0.08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 36 | 24 | 24 |
DEL PEAK 10(19P13.11) MUTATED | 0 | 4 | 1 | 0 |
DEL PEAK 10(19P13.11) WILD-TYPE | 39 | 32 | 23 | 24 |
P value = 0.00202 (Fisher's exact test), Q value = 0.0073
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 31 | 29 | 14 |
DEL PEAK 10(19P13.11) MUTATED | 0 | 0 | 2 | 3 |
DEL PEAK 10(19P13.11) WILD-TYPE | 45 | 31 | 27 | 11 |
P value = 0.00035 (Fisher's exact test), Q value = 0.0016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 42 | 20 | 10 |
DEL PEAK 10(19P13.11) MUTATED | 0 | 0 | 2 | 3 |
DEL PEAK 10(19P13.11) WILD-TYPE | 47 | 42 | 18 | 7 |
P value = 0.00487 (Fisher's exact test), Q value = 0.016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 27 | 18 | 28 | 7 | 16 | 27 |
DEL PEAK 10(19P13.11) MUTATED | 0 | 0 | 1 | 2 | 2 | 0 |
DEL PEAK 10(19P13.11) WILD-TYPE | 27 | 18 | 27 | 5 | 14 | 27 |
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 31 | 27 |
DEL PEAK 11(22Q12.1) MUTATED | 0 | 4 | 15 |
DEL PEAK 11(22Q12.1) WILD-TYPE | 65 | 27 | 12 |
P value = 0.0136 (Fisher's exact test), Q value = 0.037
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 36 | 24 | 24 |
DEL PEAK 11(22Q12.1) MUTATED | 1 | 9 | 3 | 6 |
DEL PEAK 11(22Q12.1) WILD-TYPE | 38 | 27 | 21 | 18 |
P value = 0.0133 (Fisher's exact test), Q value = 0.037
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 24 | 39 |
DEL PEAK 11(22Q12.1) MUTATED | 4 | 8 | 2 |
DEL PEAK 11(22Q12.1) WILD-TYPE | 23 | 16 | 37 |
P value = 0.0155 (Fisher's exact test), Q value = 0.038
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 31 | 29 | 14 |
DEL PEAK 11(22Q12.1) MUTATED | 2 | 5 | 8 | 4 |
DEL PEAK 11(22Q12.1) WILD-TYPE | 43 | 26 | 21 | 10 |
P value = 3e-05 (Fisher's exact test), Q value = 0.00019
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 31 | 27 |
DEL PEAK 12(22Q13.32) MUTATED | 1 | 4 | 10 |
DEL PEAK 12(22Q13.32) WILD-TYPE | 64 | 27 | 17 |
P value = 0.0304 (Fisher's exact test), Q value = 0.064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 24 | 39 |
DEL PEAK 12(22Q13.32) MUTATED | 5 | 5 | 1 |
DEL PEAK 12(22Q13.32) WILD-TYPE | 22 | 19 | 38 |
P value = 0.0249 (Fisher's exact test), Q value = 0.056
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 42 | 20 | 10 |
DEL PEAK 12(22Q13.32) MUTATED | 3 | 4 | 4 | 4 |
DEL PEAK 12(22Q13.32) WILD-TYPE | 44 | 38 | 16 | 6 |
-
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/THYM-TP/15104465/transformed.cor.cli.txt
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Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THYM-TP/15111344/THYM-TP.transferedmergedcluster.txt
-
Number of patients = 123
-
Number of significantly focal cnvs = 12
-
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.