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, 65 significant findings detected with P value < 0.05 and Q value < 0.25.
-
del_2q37.1 cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
-
del_3p22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_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 '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_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 (9.23e-05) |
1e-05 (9.23e-05) |
5e-05 (0.000316) |
0.00019 (0.00095) |
0.00201 (0.00709) |
0.00011 (6e-04) |
0.00109 (0.00451) |
0.00628 (0.0188) |
3e-05 (0.00024) |
0.00515 (0.0167) |
del 6q21 | 20 (16%) | 103 |
1e-05 (9.23e-05) |
1e-05 (9.23e-05) |
0.00023 (0.0011) |
1e-05 (9.23e-05) |
1e-05 (9.23e-05) |
1e-05 (9.23e-05) |
2e-05 (0.000171) |
0.00014 (0.00073) |
1e-05 (9.23e-05) |
5e-05 (0.000316) |
del 11q22 1 | 7 (6%) | 116 |
7e-05 (0.00042) |
1e-05 (9.23e-05) |
0.0478 (0.0899) |
0.00627 (0.0188) |
0.0313 (0.0668) |
0.0142 (0.0387) |
0.0332 (0.0686) |
0.114 (0.169) |
0.00195 (0.00709) |
0.00874 (0.025) |
del 3p22 2 | 14 (11%) | 109 |
8e-05 (0.000457) |
1e-05 (9.23e-05) |
0.0528 (0.096) |
4e-05 (3e-04) |
0.0317 (0.0668) |
0.0152 (0.0396) |
0.025 (0.0576) |
0.0659 (0.107) |
0.00046 (0.00197) |
0.0296 (0.0658) |
del 9p21 3 | 11 (9%) | 112 |
0.0166 (0.0406) |
0.00399 (0.0133) |
0.197 (0.256) |
0.0012 (0.0048) |
5e-05 (0.000316) |
1e-05 (9.23e-05) |
0.559 (0.621) |
0.00025 (0.00115) |
0.144 (0.208) |
0.0163 (0.0406) |
del 19p13 11 | 5 (4%) | 118 |
0.258 (0.31) |
0.0445 (0.0861) |
0.189 (0.255) |
0.201 (0.257) |
0.00187 (0.00701) |
0.00032 (0.00142) |
0.723 (0.755) |
0.00543 (0.0171) |
0.574 (0.632) |
0.169 (0.241) |
del 22q12 1 | 19 (15%) | 104 |
1e-05 (9.23e-05) |
0.0127 (0.0353) |
0.00797 (0.0233) |
0.0548 (0.0981) |
0.0159 (0.0406) |
0.0731 (0.117) |
0.244 (0.298) |
0.455 (0.515) |
0.52 (0.583) |
0.429 (0.49) |
del 9q22 33 | 3 (2%) | 120 |
0.604 (0.658) |
0.177 (0.244) |
0.373 (0.431) |
0.0145 (0.0388) |
0.048 (0.0899) |
0.0292 (0.0658) |
0.198 (0.256) |
0.066 (0.107) |
0.106 (0.161) |
0.0592 (0.105) |
del 10q26 3 | 6 (5%) | 117 |
0.626 (0.665) |
0.0379 (0.0772) |
0.183 (0.249) |
0.0315 (0.0668) |
0.065 (0.107) |
0.222 (0.274) |
0.74 (0.765) |
0.0655 (0.107) |
0.858 (0.88) |
0.049 (0.0904) |
del 22q13 32 | 15 (12%) | 108 |
1e-05 (9.23e-05) |
0.0863 (0.134) |
0.0441 (0.0861) |
0.0812 (0.128) |
0.0659 (0.107) |
0.0249 (0.0576) |
0.209 (0.262) |
0.299 (0.355) |
0.197 (0.256) |
0.901 (0.916) |
del 2q37 1 | 5 (4%) | 118 |
0.258 (0.31) |
0.0442 (0.0861) |
0.193 (0.256) |
0.113 (0.169) |
0.626 (0.665) |
0.305 (0.358) |
1 (1.00) |
0.0195 (0.0467) |
1 (1.00) |
0.171 (0.241) |
del 7q36 3 | 3 (2%) | 120 |
0.0606 (0.105) |
0.176 (0.244) |
0.373 (0.431) |
0.206 (0.26) |
0.00126 (0.00488) |
0.00348 (0.0119) |
0.649 (0.684) |
0.116 (0.169) |
0.106 (0.161) |
0.616 (0.665) |
P value = 0.0442 (Fisher's exact test), Q value = 0.086
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 = 0.0195 (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 = 8e-05 (Fisher's exact test), Q value = 0.00046
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 = 9.2e-05
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 = 4e-05 (Fisher's exact test), Q value = 3e-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 = 0.0317 (Fisher's exact test), Q value = 0.067
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 = 0.04
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 = 0.025 (Fisher's exact test), Q value = 0.058
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 = 0.00046 (Fisher's exact test), Q value = 0.002
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 = 0.066
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 = 9.2e-05
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 = 9.2e-05
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 = 5e-05 (Fisher's exact test), Q value = 0.00032
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 31 | 25 | 34 |
DEL PEAK 3(6P25.2) MUTATED | 15 | 5 | 1 |
DEL PEAK 3(6P25.2) WILD-TYPE | 16 | 20 | 33 |
P value = 0.00019 (Fisher's exact test), Q value = 0.00095
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 = 0.00201 (Fisher's exact test), Q value = 0.0071
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 = 0.00011 (Fisher's exact test), Q value = 6e-04
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 = 0.00109 (Fisher's exact test), Q value = 0.0045
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 = 0.00628 (Fisher's exact test), Q value = 0.019
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 = 3e-05 (Fisher's exact test), Q value = 0.00024
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 = 0.00515 (Fisher's exact test), Q value = 0.017
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 = 9.2e-05
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 = 9.2e-05
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 = 0.00023 (Fisher's exact test), Q value = 0.0011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 31 | 25 | 34 |
DEL PEAK 4(6Q21) MUTATED | 12 | 2 | 1 |
DEL PEAK 4(6Q21) WILD-TYPE | 19 | 23 | 33 |
P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05
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 = 9.2e-05
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 = 9.2e-05
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 = 0.00017
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 = 0.00014 (Fisher's exact test), Q value = 0.00073
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 = 9.2e-05
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 = 5e-05 (Fisher's exact test), Q value = 0.00032
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 = 0.00126 (Fisher's exact test), Q value = 0.0049
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 = 0.00348 (Fisher's exact test), Q value = 0.012
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 = 0.0166 (Fisher's exact test), Q value = 0.041
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 = 0.00399 (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 = 0.0012 (Fisher's exact test), Q value = 0.0048
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 = 0.00032
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 = 9.2e-05
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 = 0.00025 (Fisher's exact test), Q value = 0.0012
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 = 0.0163 (Fisher's exact test), Q value = 0.041
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 = 0.0145 (Fisher's exact test), Q value = 0.039
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 = 0.048 (Fisher's exact test), Q value = 0.09
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 = 0.0292 (Fisher's exact test), Q value = 0.066
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 = 0.0379 (Fisher's exact test), Q value = 0.077
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 = 0.0315 (Fisher's exact test), Q value = 0.067
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 = 0.049 (Fisher's exact test), Q value = 0.09
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 = 7e-05 (Fisher's exact test), Q value = 0.00042
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 = 1e-05 (Fisher's exact test), Q value = 9.2e-05
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 = 0.0478 (Fisher's exact test), Q value = 0.09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 31 | 25 | 34 |
DEL PEAK 9(11Q22.1) MUTATED | 4 | 1 | 0 |
DEL PEAK 9(11Q22.1) WILD-TYPE | 27 | 24 | 34 |
P value = 0.00627 (Fisher's exact test), Q value = 0.019
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 = 0.0313 (Fisher's exact test), Q value = 0.067
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 = 0.0142 (Fisher's exact test), Q value = 0.039
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 = 0.0332 (Fisher's exact test), Q value = 0.069
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 = 0.00195 (Fisher's exact test), Q value = 0.0071
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 = 0.00874 (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 = 0.0445 (Fisher's exact test), Q value = 0.086
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 = 0.00187 (Fisher's exact test), Q value = 0.007
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 = 0.00032 (Fisher's exact test), Q value = 0.0014
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 = 0.00543 (Fisher's exact test), Q value = 0.017
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 = 9.2e-05
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 = 0.0127 (Fisher's exact test), Q value = 0.035
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 = 0.00797 (Fisher's exact test), Q value = 0.023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 31 | 25 | 34 |
DEL PEAK 11(22Q12.1) MUTATED | 5 | 8 | 1 |
DEL PEAK 11(22Q12.1) WILD-TYPE | 26 | 17 | 33 |
P value = 0.0159 (Fisher's exact test), Q value = 0.041
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 = 1e-05 (Fisher's exact test), Q value = 9.2e-05
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 = 0.0441 (Fisher's exact test), Q value = 0.086
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 31 | 25 | 34 |
DEL PEAK 12(22Q13.32) MUTATED | 4 | 6 | 1 |
DEL PEAK 12(22Q13.32) WILD-TYPE | 27 | 19 | 33 |
P value = 0.0249 (Fisher's exact test), Q value = 0.058
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/19781936/transformed.cor.cli.txt
-
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THYM-TP/20140903/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.