This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 9 genes and 10 molecular subtypes across 178 patients, 32 significant findings detected with P value < 0.05 and Q value < 0.25.
-
HRAS mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
EPAS1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
NF1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
RET mutation correlated to 'CN_CNMF'.
-
CSDE1 mutation correlated to 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_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 |
||
nMutated (%) | 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 | |
HRAS | 18 (10%) | 160 |
1e-05 (3e-04) |
6e-05 (0.00103) |
0.0546 (0.149) |
0.00116 (0.00746) |
1e-05 (3e-04) |
1e-05 (3e-04) |
5e-05 (0.00103) |
0.00024 (0.00216) |
8e-05 (0.00103) |
0.00039 (0.00292) |
EPAS1 | 8 (4%) | 170 |
0.0112 (0.0337) |
0.0059 (0.0229) |
0.00789 (0.0263) |
0.355 (0.627) |
0.00176 (0.0088) |
0.00134 (0.00793) |
0.00169 (0.0088) |
0.0171 (0.0496) |
0.00038 (0.00292) |
0.00192 (0.00909) |
NF1 | 15 (8%) | 163 |
0.00016 (0.0017) |
0.00062 (0.00429) |
0.0422 (0.119) |
0.0886 (0.217) |
0.00973 (0.0306) |
8e-05 (0.00103) |
0.00017 (0.0017) |
0.00673 (0.0242) |
0.00986 (0.0306) |
0.00141 (0.00793) |
CSDE1 | 4 (2%) | 174 |
0.283 (0.565) |
0.58 (0.829) |
0.489 (0.758) |
0.00493 (0.0222) |
0.35 (0.627) |
0.00564 (0.0229) |
0.00763 (0.0263) |
0.00612 (0.0229) |
||
RET | 6 (3%) | 172 |
0.0054 (0.0229) |
0.486 (0.758) |
0.207 (0.454) |
0.324 (0.627) |
0.0892 (0.217) |
0.104 (0.239) |
0.436 (0.728) |
0.0676 (0.174) |
0.258 (0.527) |
0.183 (0.411) |
GPR128 | 4 (2%) | 174 |
1 (1.00) |
0.101 (0.239) |
0.89 (1.00) |
0.888 (1.00) |
0.545 (0.803) |
0.776 (0.995) |
0.527 (0.803) |
0.553 (0.803) |
||
AMMECR1 | 3 (2%) | 175 |
0.788 (0.995) |
1 (1.00) |
0.348 (0.627) |
1 (1.00) |
0.244 (0.511) |
0.628 (0.867) |
0.796 (0.995) |
1 (1.00) |
0.594 (0.835) |
0.79 (0.995) |
SHROOM4 | 3 (2%) | 175 |
1 (1.00) |
0.47 (0.755) |
0.538 (0.803) |
1 (1.00) |
0.678 (0.911) |
0.723 (0.958) |
0.636 (0.867) |
|||
FAM83D | 3 (2%) | 175 |
0.348 (0.627) |
0.334 (0.627) |
0.409 (0.708) |
0.462 (0.755) |
0.0579 (0.153) |
0.818 (1.00) |
0.227 (0.486) |
0.437 (0.728) |
P value = 1e-05 (Fisher's exact test), Q value = 3e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 60 | 63 | 38 |
HRAS MUTATED | 14 | 0 | 1 |
HRAS WILD-TYPE | 46 | 63 | 37 |
P value = 6e-05 (Fisher's exact test), Q value = 0.001
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 85 | 49 |
HRAS MUTATED | 0 | 17 | 1 |
HRAS WILD-TYPE | 44 | 68 | 48 |
P value = 0.0546 (Fisher's exact test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 9 | 20 | 6 | 17 | 13 |
HRAS MUTATED | 3 | 2 | 5 | 0 | 0 | 0 |
HRAS WILD-TYPE | 11 | 7 | 15 | 6 | 17 | 13 |
P value = 0.00116 (Fisher's exact test), Q value = 0.0075
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 18 | 28 |
HRAS MUTATED | 1 | 7 | 2 |
HRAS WILD-TYPE | 32 | 11 | 26 |
P value = 1e-05 (Fisher's exact test), Q value = 3e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 69 | 49 | 21 |
HRAS MUTATED | 0 | 18 | 0 | 0 |
HRAS WILD-TYPE | 39 | 51 | 49 | 21 |
P value = 1e-05 (Fisher's exact test), Q value = 3e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 71 | 48 | 21 |
HRAS MUTATED | 0 | 18 | 0 | 0 |
HRAS WILD-TYPE | 38 | 53 | 48 | 21 |
P value = 5e-05 (Fisher's exact test), Q value = 0.001
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 65 | 39 |
HRAS MUTATED | 1 | 15 | 2 |
HRAS WILD-TYPE | 73 | 50 | 37 |
P value = 0.00024 (Fisher's exact test), Q value = 0.0022
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 76 | 59 | 18 | 25 |
HRAS MUTATED | 1 | 14 | 1 | 2 |
HRAS WILD-TYPE | 75 | 45 | 17 | 23 |
P value = 8e-05 (Fisher's exact test), Q value = 0.001
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 64 | 12 | 41 | 24 |
HRAS MUTATED | 1 | 15 | 2 | 0 | 0 |
HRAS WILD-TYPE | 35 | 49 | 10 | 41 | 24 |
P value = 0.00039 (Fisher's exact test), Q value = 0.0029
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 80 | 60 | 18 | 19 |
HRAS MUTATED | 16 | 0 | 1 | 1 |
HRAS WILD-TYPE | 64 | 60 | 17 | 18 |
P value = 0.0112 (Fisher's exact test), Q value = 0.034
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 60 | 63 | 38 |
EPAS1 MUTATED | 0 | 7 | 1 |
EPAS1 WILD-TYPE | 60 | 56 | 37 |
P value = 0.0059 (Fisher's exact test), Q value = 0.023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 85 | 49 |
EPAS1 MUTATED | 4 | 0 | 4 |
EPAS1 WILD-TYPE | 40 | 85 | 45 |
P value = 0.00789 (Fisher's exact test), Q value = 0.026
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 9 | 20 | 6 | 17 | 13 |
EPAS1 MUTATED | 1 | 0 | 0 | 0 | 0 | 4 |
EPAS1 WILD-TYPE | 13 | 9 | 20 | 6 | 17 | 9 |
P value = 0.355 (Fisher's exact test), Q value = 0.63
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 18 | 28 |
EPAS1 MUTATED | 2 | 0 | 3 |
EPAS1 WILD-TYPE | 31 | 18 | 25 |
P value = 0.00176 (Fisher's exact test), Q value = 0.0088
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 69 | 49 | 21 |
EPAS1 MUTATED | 1 | 0 | 7 | 0 |
EPAS1 WILD-TYPE | 38 | 69 | 42 | 21 |
P value = 0.00134 (Fisher's exact test), Q value = 0.0079
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 71 | 48 | 21 |
EPAS1 MUTATED | 1 | 0 | 7 | 0 |
EPAS1 WILD-TYPE | 37 | 71 | 41 | 21 |
P value = 0.00169 (Fisher's exact test), Q value = 0.0088
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 65 | 39 |
EPAS1 MUTATED | 8 | 0 | 0 |
EPAS1 WILD-TYPE | 66 | 65 | 39 |
P value = 0.0171 (Fisher's exact test), Q value = 0.05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 76 | 59 | 18 | 25 |
EPAS1 MUTATED | 8 | 0 | 0 | 0 |
EPAS1 WILD-TYPE | 68 | 59 | 18 | 25 |
P value = 0.00038 (Fisher's exact test), Q value = 0.0029
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 64 | 12 | 41 | 24 |
EPAS1 MUTATED | 0 | 0 | 1 | 7 | 0 |
EPAS1 WILD-TYPE | 36 | 64 | 11 | 34 | 24 |
P value = 0.00192 (Fisher's exact test), Q value = 0.0091
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 80 | 60 | 18 | 19 |
EPAS1 MUTATED | 0 | 8 | 0 | 0 |
EPAS1 WILD-TYPE | 80 | 52 | 18 | 19 |
P value = 0.00016 (Fisher's exact test), Q value = 0.0017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 60 | 63 | 38 |
NF1 MUTATED | 3 | 1 | 10 |
NF1 WILD-TYPE | 57 | 62 | 28 |
P value = 0.00062 (Fisher's exact test), Q value = 0.0043
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 85 | 49 |
NF1 MUTATED | 0 | 14 | 1 |
NF1 WILD-TYPE | 44 | 71 | 48 |
P value = 0.0422 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 9 | 20 | 6 | 17 | 13 |
NF1 MUTATED | 2 | 1 | 6 | 0 | 0 | 0 |
NF1 WILD-TYPE | 12 | 8 | 14 | 6 | 17 | 13 |
P value = 0.0886 (Fisher's exact test), Q value = 0.22
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 18 | 28 |
NF1 MUTATED | 1 | 4 | 4 |
NF1 WILD-TYPE | 32 | 14 | 24 |
P value = 0.00973 (Fisher's exact test), Q value = 0.031
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 69 | 49 | 21 |
NF1 MUTATED | 3 | 11 | 0 | 1 |
NF1 WILD-TYPE | 36 | 58 | 49 | 20 |
P value = 8e-05 (Fisher's exact test), Q value = 0.001
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 71 | 48 | 21 |
NF1 MUTATED | 0 | 14 | 0 | 1 |
NF1 WILD-TYPE | 38 | 57 | 48 | 20 |
P value = 0.00017 (Fisher's exact test), Q value = 0.0017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 65 | 39 |
NF1 MUTATED | 1 | 13 | 1 |
NF1 WILD-TYPE | 73 | 52 | 38 |
P value = 0.00673 (Fisher's exact test), Q value = 0.024
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 76 | 59 | 18 | 25 |
NF1 MUTATED | 2 | 11 | 0 | 2 |
NF1 WILD-TYPE | 74 | 48 | 18 | 23 |
P value = 0.00986 (Fisher's exact test), Q value = 0.031
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 64 | 12 | 41 | 24 |
NF1 MUTATED | 3 | 10 | 2 | 0 | 0 |
NF1 WILD-TYPE | 33 | 54 | 10 | 41 | 24 |
P value = 0.00141 (Fisher's exact test), Q value = 0.0079
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 80 | 60 | 18 | 19 |
NF1 MUTATED | 13 | 0 | 0 | 2 |
NF1 WILD-TYPE | 67 | 60 | 18 | 17 |
P value = 0.0054 (Fisher's exact test), Q value = 0.023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 60 | 63 | 38 |
RET MUTATED | 6 | 0 | 0 |
RET WILD-TYPE | 54 | 63 | 38 |
P value = 0.486 (Fisher's exact test), Q value = 0.76
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 85 | 49 |
RET MUTATED | 0 | 4 | 2 |
RET WILD-TYPE | 44 | 81 | 47 |
P value = 0.207 (Fisher's exact test), Q value = 0.45
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 9 | 20 | 6 | 17 | 13 |
RET MUTATED | 0 | 0 | 3 | 0 | 0 | 0 |
RET WILD-TYPE | 14 | 9 | 17 | 6 | 17 | 13 |
P value = 0.324 (Fisher's exact test), Q value = 0.63
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 18 | 28 |
RET MUTATED | 0 | 1 | 2 |
RET WILD-TYPE | 33 | 17 | 26 |
P value = 0.0892 (Fisher's exact test), Q value = 0.22
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 69 | 49 | 21 |
RET MUTATED | 0 | 5 | 0 | 1 |
RET WILD-TYPE | 39 | 64 | 49 | 20 |
P value = 0.104 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 71 | 48 | 21 |
RET MUTATED | 0 | 5 | 0 | 1 |
RET WILD-TYPE | 38 | 66 | 48 | 20 |
P value = 0.436 (Fisher's exact test), Q value = 0.73
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 65 | 39 |
RET MUTATED | 1 | 3 | 2 |
RET WILD-TYPE | 73 | 62 | 37 |
P value = 0.0676 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 76 | 59 | 18 | 25 |
RET MUTATED | 0 | 4 | 1 | 1 |
RET WILD-TYPE | 76 | 55 | 17 | 24 |
P value = 0.258 (Fisher's exact test), Q value = 0.53
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 64 | 12 | 41 | 24 |
RET MUTATED | 1 | 4 | 1 | 0 | 0 |
RET WILD-TYPE | 35 | 60 | 11 | 41 | 24 |
P value = 0.183 (Fisher's exact test), Q value = 0.41
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 80 | 60 | 18 | 19 |
RET MUTATED | 4 | 0 | 1 | 1 |
RET WILD-TYPE | 76 | 60 | 17 | 18 |
P value = 0.283 (Fisher's exact test), Q value = 0.57
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 60 | 63 | 38 |
CSDE1 MUTATED | 0 | 3 | 1 |
CSDE1 WILD-TYPE | 60 | 60 | 37 |
P value = 0.58 (Fisher's exact test), Q value = 0.83
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 85 | 49 |
CSDE1 MUTATED | 1 | 3 | 0 |
CSDE1 WILD-TYPE | 43 | 82 | 49 |
P value = 0.489 (Fisher's exact test), Q value = 0.76
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 69 | 49 | 21 |
CSDE1 MUTATED | 1 | 3 | 0 | 0 |
CSDE1 WILD-TYPE | 38 | 66 | 49 | 21 |
P value = 0.00493 (Fisher's exact test), Q value = 0.022
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 71 | 48 | 21 |
CSDE1 MUTATED | 4 | 0 | 0 | 0 |
CSDE1 WILD-TYPE | 34 | 71 | 48 | 21 |
P value = 0.35 (Fisher's exact test), Q value = 0.63
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 65 | 39 |
CSDE1 MUTATED | 1 | 3 | 0 |
CSDE1 WILD-TYPE | 73 | 62 | 39 |
P value = 0.00564 (Fisher's exact test), Q value = 0.023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 76 | 59 | 18 | 25 |
CSDE1 MUTATED | 1 | 0 | 3 | 0 |
CSDE1 WILD-TYPE | 75 | 59 | 15 | 25 |
P value = 0.00763 (Fisher's exact test), Q value = 0.026
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 64 | 12 | 41 | 24 |
CSDE1 MUTATED | 4 | 0 | 0 | 0 | 0 |
CSDE1 WILD-TYPE | 32 | 64 | 12 | 41 | 24 |
P value = 0.00612 (Fisher's exact test), Q value = 0.023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 80 | 60 | 18 | 19 |
CSDE1 MUTATED | 1 | 0 | 3 | 0 |
CSDE1 WILD-TYPE | 79 | 60 | 15 | 19 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 60 | 63 | 38 |
GPR128 MUTATED | 1 | 1 | 1 |
GPR128 WILD-TYPE | 59 | 62 | 37 |
P value = 0.101 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 85 | 49 |
GPR128 MUTATED | 3 | 1 | 0 |
GPR128 WILD-TYPE | 41 | 84 | 49 |
P value = 0.89 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 69 | 49 | 21 |
GPR128 MUTATED | 1 | 1 | 2 | 0 |
GPR128 WILD-TYPE | 38 | 68 | 47 | 21 |
P value = 0.888 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 71 | 48 | 21 |
GPR128 MUTATED | 1 | 1 | 2 | 0 |
GPR128 WILD-TYPE | 37 | 70 | 46 | 21 |
P value = 0.545 (Fisher's exact test), Q value = 0.8
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 65 | 39 |
GPR128 MUTATED | 3 | 1 | 0 |
GPR128 WILD-TYPE | 71 | 64 | 39 |
P value = 0.776 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 76 | 59 | 18 | 25 |
GPR128 MUTATED | 3 | 1 | 0 | 0 |
GPR128 WILD-TYPE | 73 | 58 | 18 | 25 |
P value = 0.527 (Fisher's exact test), Q value = 0.8
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 64 | 12 | 41 | 24 |
GPR128 MUTATED | 0 | 1 | 0 | 2 | 1 |
GPR128 WILD-TYPE | 36 | 63 | 12 | 39 | 23 |
P value = 0.553 (Fisher's exact test), Q value = 0.8
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 80 | 60 | 18 | 19 |
GPR128 MUTATED | 1 | 3 | 0 | 0 |
GPR128 WILD-TYPE | 79 | 57 | 18 | 19 |
P value = 0.788 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 60 | 63 | 38 |
AMMECR1 MUTATED | 1 | 2 | 0 |
AMMECR1 WILD-TYPE | 59 | 61 | 38 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 85 | 49 |
AMMECR1 MUTATED | 1 | 1 | 1 |
AMMECR1 WILD-TYPE | 43 | 84 | 48 |
P value = 0.348 (Fisher's exact test), Q value = 0.63
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 9 | 20 | 6 | 17 | 13 |
AMMECR1 MUTATED | 0 | 0 | 1 | 1 | 0 | 1 |
AMMECR1 WILD-TYPE | 14 | 9 | 19 | 5 | 17 | 12 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 18 | 28 |
AMMECR1 MUTATED | 1 | 1 | 1 |
AMMECR1 WILD-TYPE | 32 | 17 | 27 |
P value = 0.244 (Fisher's exact test), Q value = 0.51
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 69 | 49 | 21 |
AMMECR1 MUTATED | 1 | 0 | 2 | 0 |
AMMECR1 WILD-TYPE | 38 | 69 | 47 | 21 |
P value = 0.628 (Fisher's exact test), Q value = 0.87
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 71 | 48 | 21 |
AMMECR1 MUTATED | 0 | 1 | 2 | 0 |
AMMECR1 WILD-TYPE | 38 | 70 | 46 | 21 |
P value = 0.796 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 65 | 39 |
AMMECR1 MUTATED | 2 | 1 | 0 |
AMMECR1 WILD-TYPE | 72 | 64 | 39 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 76 | 59 | 18 | 25 |
AMMECR1 MUTATED | 2 | 1 | 0 | 0 |
AMMECR1 WILD-TYPE | 74 | 58 | 18 | 25 |
P value = 0.594 (Fisher's exact test), Q value = 0.84
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 64 | 12 | 41 | 24 |
AMMECR1 MUTATED | 0 | 1 | 0 | 2 | 0 |
AMMECR1 WILD-TYPE | 36 | 63 | 12 | 39 | 24 |
P value = 0.79 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 80 | 60 | 18 | 19 |
AMMECR1 MUTATED | 1 | 2 | 0 | 0 |
AMMECR1 WILD-TYPE | 79 | 58 | 18 | 19 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 85 | 49 |
SHROOM4 MUTATED | 1 | 1 | 1 |
SHROOM4 WILD-TYPE | 43 | 84 | 48 |
P value = 0.47 (Fisher's exact test), Q value = 0.76
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 69 | 49 | 21 |
SHROOM4 MUTATED | 1 | 1 | 0 | 1 |
SHROOM4 WILD-TYPE | 38 | 68 | 49 | 20 |
P value = 0.538 (Fisher's exact test), Q value = 0.8
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 71 | 48 | 21 |
SHROOM4 MUTATED | 0 | 1 | 1 | 1 |
SHROOM4 WILD-TYPE | 38 | 70 | 47 | 20 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 65 | 39 |
SHROOM4 MUTATED | 1 | 1 | 1 |
SHROOM4 WILD-TYPE | 73 | 64 | 38 |
P value = 0.678 (Fisher's exact test), Q value = 0.91
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 76 | 59 | 18 | 25 |
SHROOM4 MUTATED | 1 | 1 | 0 | 1 |
SHROOM4 WILD-TYPE | 75 | 58 | 18 | 24 |
P value = 0.723 (Fisher's exact test), Q value = 0.96
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 64 | 12 | 41 | 24 |
SHROOM4 MUTATED | 0 | 1 | 0 | 1 | 1 |
SHROOM4 WILD-TYPE | 36 | 63 | 12 | 40 | 23 |
P value = 0.636 (Fisher's exact test), Q value = 0.87
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 80 | 60 | 18 | 19 |
SHROOM4 MUTATED | 1 | 1 | 0 | 1 |
SHROOM4 WILD-TYPE | 79 | 59 | 18 | 18 |
P value = 0.348 (Fisher's exact test), Q value = 0.63
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 60 | 63 | 38 |
FAM83D MUTATED | 2 | 0 | 1 |
FAM83D WILD-TYPE | 58 | 63 | 37 |
P value = 0.334 (Fisher's exact test), Q value = 0.63
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 85 | 49 |
FAM83D MUTATED | 0 | 3 | 0 |
FAM83D WILD-TYPE | 44 | 82 | 49 |
P value = 0.409 (Fisher's exact test), Q value = 0.71
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 69 | 49 | 21 |
FAM83D MUTATED | 0 | 3 | 0 | 0 |
FAM83D WILD-TYPE | 39 | 66 | 49 | 21 |
P value = 0.462 (Fisher's exact test), Q value = 0.76
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 71 | 48 | 21 |
FAM83D MUTATED | 0 | 3 | 0 | 0 |
FAM83D WILD-TYPE | 38 | 68 | 48 | 21 |
P value = 0.0579 (Fisher's exact test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 65 | 39 |
FAM83D MUTATED | 0 | 3 | 0 |
FAM83D WILD-TYPE | 74 | 62 | 39 |
P value = 0.818 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 76 | 59 | 18 | 25 |
FAM83D MUTATED | 1 | 2 | 0 | 0 |
FAM83D WILD-TYPE | 75 | 57 | 18 | 25 |
P value = 0.227 (Fisher's exact test), Q value = 0.49
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 64 | 12 | 41 | 24 |
FAM83D MUTATED | 0 | 2 | 1 | 0 | 0 |
FAM83D WILD-TYPE | 36 | 62 | 11 | 41 | 24 |
P value = 0.437 (Fisher's exact test), Q value = 0.73
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 80 | 60 | 18 | 19 |
FAM83D MUTATED | 3 | 0 | 0 | 0 |
FAM83D WILD-TYPE | 77 | 60 | 18 | 19 |
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Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline
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Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PCPG-TP/15165019/transformed.cor.cli.txt
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Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PCPG-TP/15107813/PCPG-TP.transferedmergedcluster.txt
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Number of patients = 178
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Number of significantly mutated genes = 9
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Number of Molecular subtypes = 10
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Exclude genes that fewer than K tumors have mutations, 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.