This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 12 genes and 9 molecular subtypes across 69 patients, 3 significant findings detected with P value < 0.05 and Q value < 0.25.
-
TP53 mutation correlated to 'MRNA_CNMF'.
-
KRAS mutation correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Clinical Features |
MRNA CNMF |
MRNA CHIERARCHICAL |
CN CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ 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 | |
KRAS | 38 (55%) | 31 |
0.249 (1.00) |
0.00752 (0.729) |
0.00131 (0.13) |
0.833 (1.00) |
0.852 (1.00) |
0.0465 (1.00) |
0.00019 (0.019) |
0.291 (1.00) |
0.00564 (0.553) |
TP53 | 44 (64%) | 25 |
0.00015 (0.0151) |
0.015 (1.00) |
0.532 (1.00) |
0.162 (1.00) |
0.839 (1.00) |
0.487 (1.00) |
0.652 (1.00) |
1 (1.00) |
0.146 (1.00) |
APC | 56 (81%) | 13 |
0.925 (1.00) |
0.916 (1.00) |
0.405 (1.00) |
0.361 (1.00) |
0.384 (1.00) |
0.242 (1.00) |
1 (1.00) |
0.452 (1.00) |
0.624 (1.00) |
SMAD4 | 8 (12%) | 61 |
0.078 (1.00) |
0.777 (1.00) |
0.893 (1.00) |
0.156 (1.00) |
0.055 (1.00) |
0.186 (1.00) |
0.228 (1.00) |
0.311 (1.00) |
0.263 (1.00) |
FBXW7 | 9 (13%) | 60 |
0.19 (1.00) |
0.409 (1.00) |
0.434 (1.00) |
0.689 (1.00) |
0.633 (1.00) |
1 (1.00) |
0.119 (1.00) |
0.806 (1.00) |
0.577 (1.00) |
NRAS | 5 (7%) | 64 |
1 (1.00) |
0.839 (1.00) |
0.111 (1.00) |
1 (1.00) |
1 (1.00) |
0.0977 (1.00) |
1 (1.00) |
||
ARID1A | 5 (7%) | 64 |
0.364 (1.00) |
0.393 (1.00) |
0.525 (1.00) |
0.171 (1.00) |
0.532 (1.00) |
1 (1.00) |
1 (1.00) |
0.314 (1.00) |
0.256 (1.00) |
RBM10 | 4 (6%) | 65 |
1 (1.00) |
0.789 (1.00) |
0.469 (1.00) |
1 (1.00) |
0.78 (1.00) |
0.0164 (1.00) |
0.0443 (1.00) |
0.533 (1.00) |
0.566 (1.00) |
TCF7L2 | 7 (10%) | 62 |
0.78 (1.00) |
0.204 (1.00) |
0.227 (1.00) |
0.15 (1.00) |
0.292 (1.00) |
1 (1.00) |
0.306 (1.00) |
1 (1.00) |
0.69 (1.00) |
ERBB2 | 4 (6%) | 65 |
1 (1.00) |
0.877 (1.00) |
0.469 (1.00) |
0.675 (1.00) |
0.409 (1.00) |
0.0308 (1.00) |
0.0349 (1.00) |
1 (1.00) |
1 (1.00) |
KIAA1804 | 9 (13%) | 60 |
0.512 (1.00) |
0.837 (1.00) |
0.474 (1.00) |
1 (1.00) |
0.599 (1.00) |
1 (1.00) |
0.758 (1.00) |
0.804 (1.00) |
0.574 (1.00) |
CCDC88C | 3 (4%) | 66 |
1 (1.00) |
0.593 (1.00) |
0.432 (1.00) |
0.466 (1.00) |
P value = 0.925 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 21 | 19 |
APC MUTATED | 19 | 16 | 16 |
APC WILD-TYPE | 5 | 5 | 3 |
P value = 0.916 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2 |
APC MUTATED | 4 | 10 | 8 | 8 | 5 | 7 | 7 | 2 |
APC WILD-TYPE | 2 | 2 | 4 | 1 | 1 | 2 | 1 | 0 |
P value = 0.405 (Fisher's exact test), Q value = 1
nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|
ALL | 17 | 18 | 17 | 11 | 5 |
APC MUTATED | 11 | 16 | 15 | 9 | 4 |
APC WILD-TYPE | 6 | 2 | 2 | 2 | 1 |
P value = 0.361 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 16 | 14 | 23 |
APC MUTATED | 11 | 12 | 20 |
APC WILD-TYPE | 5 | 2 | 3 |
P value = 0.384 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 20 | 9 | 14 | 2 | 8 |
APC MUTATED | 15 | 7 | 12 | 1 | 8 |
APC WILD-TYPE | 5 | 2 | 2 | 1 | 0 |
P value = 0.242 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 1 | 4 | 2 | 61 |
APC MUTATED | 0 | 4 | 2 | 50 |
APC WILD-TYPE | 1 | 0 | 0 | 11 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|
ALL | 1 | 38 | 29 |
APC MUTATED | 1 | 31 | 24 |
APC WILD-TYPE | 0 | 7 | 5 |
P value = 0.452 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|
ALL | 2 | 3 | 6 | 54 |
APC MUTATED | 1 | 3 | 5 | 45 |
APC WILD-TYPE | 1 | 0 | 1 | 9 |
P value = 0.624 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 9 | 3 | 53 |
APC MUTATED | 8 | 2 | 44 |
APC WILD-TYPE | 1 | 1 | 9 |
P value = 0.00015 (Fisher's exact test), Q value = 0.015
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 21 | 19 |
TP53 MUTATED | 7 | 15 | 17 |
TP53 WILD-TYPE | 17 | 6 | 2 |
P value = 0.015 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2 |
TP53 MUTATED | 2 | 8 | 4 | 9 | 5 | 6 | 5 | 0 |
TP53 WILD-TYPE | 4 | 4 | 8 | 0 | 1 | 3 | 3 | 2 |
P value = 0.532 (Fisher's exact test), Q value = 1
nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|
ALL | 17 | 18 | 17 | 11 | 5 |
TP53 MUTATED | 13 | 9 | 10 | 8 | 3 |
TP53 WILD-TYPE | 4 | 9 | 7 | 3 | 2 |
P value = 0.162 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 16 | 14 | 23 |
TP53 MUTATED | 10 | 12 | 13 |
TP53 WILD-TYPE | 6 | 2 | 10 |
P value = 0.839 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 20 | 9 | 14 | 2 | 8 |
TP53 MUTATED | 12 | 7 | 9 | 1 | 6 |
TP53 WILD-TYPE | 8 | 2 | 5 | 1 | 2 |
P value = 0.487 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 1 | 4 | 2 | 61 |
TP53 MUTATED | 0 | 2 | 1 | 40 |
TP53 WILD-TYPE | 1 | 2 | 1 | 21 |
P value = 0.652 (Fisher's exact test), Q value = 1
nPatients | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|
ALL | 1 | 38 | 29 |
TP53 MUTATED | 1 | 22 | 20 |
TP53 WILD-TYPE | 0 | 16 | 9 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|
ALL | 2 | 3 | 6 | 54 |
TP53 MUTATED | 1 | 2 | 4 | 34 |
TP53 WILD-TYPE | 1 | 1 | 2 | 20 |
P value = 0.146 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 9 | 3 | 53 |
TP53 MUTATED | 8 | 1 | 32 |
TP53 WILD-TYPE | 1 | 2 | 21 |
P value = 0.249 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 21 | 19 |
KRAS MUTATED | 16 | 11 | 8 |
KRAS WILD-TYPE | 8 | 10 | 11 |
P value = 0.00752 (Fisher's exact test), Q value = 0.73
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2 |
KRAS MUTATED | 3 | 9 | 9 | 3 | 3 | 6 | 0 | 2 |
KRAS WILD-TYPE | 3 | 3 | 3 | 6 | 3 | 3 | 8 | 0 |
P value = 0.00131 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|
ALL | 17 | 18 | 17 | 11 | 5 |
KRAS MUTATED | 3 | 13 | 9 | 8 | 5 |
KRAS WILD-TYPE | 14 | 5 | 8 | 3 | 0 |
P value = 0.833 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 16 | 14 | 23 |
KRAS MUTATED | 7 | 8 | 12 |
KRAS WILD-TYPE | 9 | 6 | 11 |
P value = 0.852 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 20 | 9 | 14 | 2 | 8 |
KRAS MUTATED | 9 | 4 | 9 | 1 | 4 |
KRAS WILD-TYPE | 11 | 5 | 5 | 1 | 4 |
P value = 0.0465 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 1 | 4 | 2 | 61 |
KRAS MUTATED | 1 | 4 | 0 | 32 |
KRAS WILD-TYPE | 0 | 0 | 2 | 29 |
P value = 0.00019 (Fisher's exact test), Q value = 0.019
nPatients | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|
ALL | 1 | 38 | 29 |
KRAS MUTATED | 1 | 28 | 8 |
KRAS WILD-TYPE | 0 | 10 | 21 |
P value = 0.291 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|
ALL | 2 | 3 | 6 | 54 |
KRAS MUTATED | 1 | 2 | 1 | 30 |
KRAS WILD-TYPE | 1 | 1 | 5 | 24 |
P value = 0.00564 (Fisher's exact test), Q value = 0.55
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 9 | 3 | 53 |
KRAS MUTATED | 1 | 3 | 30 |
KRAS WILD-TYPE | 8 | 0 | 23 |
P value = 0.078 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 21 | 19 |
SMAD4 MUTATED | 5 | 0 | 2 |
SMAD4 WILD-TYPE | 19 | 21 | 17 |
P value = 0.777 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2 |
SMAD4 MUTATED | 0 | 3 | 2 | 1 | 0 | 1 | 0 | 0 |
SMAD4 WILD-TYPE | 6 | 9 | 10 | 8 | 6 | 8 | 8 | 2 |
P value = 0.893 (Fisher's exact test), Q value = 1
nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|
ALL | 17 | 18 | 17 | 11 | 5 |
SMAD4 MUTATED | 1 | 3 | 2 | 1 | 1 |
SMAD4 WILD-TYPE | 16 | 15 | 15 | 10 | 4 |
P value = 0.156 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 16 | 14 | 23 |
SMAD4 MUTATED | 0 | 3 | 4 |
SMAD4 WILD-TYPE | 16 | 11 | 19 |
P value = 0.055 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 20 | 9 | 14 | 2 | 8 |
SMAD4 MUTATED | 0 | 3 | 3 | 0 | 1 |
SMAD4 WILD-TYPE | 20 | 6 | 11 | 2 | 7 |
P value = 0.186 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 1 | 4 | 2 | 61 |
SMAD4 MUTATED | 1 | 0 | 0 | 7 |
SMAD4 WILD-TYPE | 0 | 4 | 2 | 54 |
P value = 0.228 (Fisher's exact test), Q value = 1
nPatients | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|
ALL | 1 | 38 | 29 |
SMAD4 MUTATED | 0 | 7 | 1 |
SMAD4 WILD-TYPE | 1 | 31 | 28 |
P value = 0.311 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|
ALL | 2 | 3 | 6 | 54 |
SMAD4 MUTATED | 1 | 0 | 0 | 7 |
SMAD4 WILD-TYPE | 1 | 3 | 6 | 47 |
P value = 0.263 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 9 | 3 | 53 |
SMAD4 MUTATED | 0 | 1 | 7 |
SMAD4 WILD-TYPE | 9 | 2 | 46 |
P value = 0.19 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 21 | 19 |
FBXW7 MUTATED | 2 | 5 | 1 |
FBXW7 WILD-TYPE | 22 | 16 | 18 |
P value = 0.409 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2 |
FBXW7 MUTATED | 0 | 3 | 1 | 1 | 0 | 3 | 0 | 0 |
FBXW7 WILD-TYPE | 6 | 9 | 11 | 8 | 6 | 6 | 8 | 2 |
P value = 0.434 (Fisher's exact test), Q value = 1
nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|
ALL | 17 | 18 | 17 | 11 | 5 |
FBXW7 MUTATED | 2 | 3 | 4 | 0 | 0 |
FBXW7 WILD-TYPE | 15 | 15 | 13 | 11 | 5 |
P value = 0.689 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 16 | 14 | 23 |
FBXW7 MUTATED | 3 | 2 | 2 |
FBXW7 WILD-TYPE | 13 | 12 | 21 |
P value = 0.633 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 20 | 9 | 14 | 2 | 8 |
FBXW7 MUTATED | 2 | 2 | 1 | 0 | 2 |
FBXW7 WILD-TYPE | 18 | 7 | 13 | 2 | 6 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 1 | 4 | 2 | 61 |
FBXW7 MUTATED | 0 | 0 | 0 | 9 |
FBXW7 WILD-TYPE | 1 | 4 | 2 | 52 |
P value = 0.119 (Fisher's exact test), Q value = 1
nPatients | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|
ALL | 1 | 38 | 29 |
FBXW7 MUTATED | 0 | 8 | 1 |
FBXW7 WILD-TYPE | 1 | 30 | 28 |
P value = 0.806 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|
ALL | 2 | 3 | 6 | 54 |
FBXW7 MUTATED | 0 | 0 | 0 | 9 |
FBXW7 WILD-TYPE | 2 | 3 | 6 | 45 |
P value = 0.577 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 9 | 3 | 53 |
FBXW7 MUTATED | 0 | 0 | 9 |
FBXW7 WILD-TYPE | 9 | 3 | 44 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 21 | 19 |
NRAS MUTATED | 2 | 2 | 1 |
NRAS WILD-TYPE | 22 | 19 | 18 |
P value = 0.839 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2 |
NRAS MUTATED | 1 | 2 | 1 | 1 | 0 | 0 | 0 | 0 |
NRAS WILD-TYPE | 5 | 10 | 11 | 8 | 6 | 9 | 8 | 2 |
P value = 0.111 (Fisher's exact test), Q value = 1
nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|
ALL | 17 | 18 | 17 | 11 | 5 |
NRAS MUTATED | 0 | 3 | 0 | 2 | 0 |
NRAS WILD-TYPE | 17 | 15 | 17 | 9 | 5 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 1 | 4 | 2 | 61 |
NRAS MUTATED | 0 | 0 | 0 | 5 |
NRAS WILD-TYPE | 1 | 4 | 2 | 56 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|
ALL | 1 | 38 | 29 |
NRAS MUTATED | 0 | 3 | 2 |
NRAS WILD-TYPE | 1 | 35 | 27 |
P value = 0.0977 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|
ALL | 2 | 3 | 6 | 54 |
NRAS MUTATED | 1 | 0 | 1 | 3 |
NRAS WILD-TYPE | 1 | 3 | 5 | 51 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 9 | 3 | 53 |
NRAS MUTATED | 0 | 0 | 5 |
NRAS WILD-TYPE | 9 | 3 | 48 |
P value = 0.364 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 21 | 19 |
ARID1A MUTATED | 3 | 2 | 0 |
ARID1A WILD-TYPE | 21 | 19 | 19 |
P value = 0.393 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2 |
ARID1A MUTATED | 1 | 1 | 1 | 0 | 0 | 1 | 0 | 1 |
ARID1A WILD-TYPE | 5 | 11 | 11 | 9 | 6 | 8 | 8 | 1 |
P value = 0.525 (Fisher's exact test), Q value = 1
nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|
ALL | 17 | 18 | 17 | 11 | 5 |
ARID1A MUTATED | 1 | 3 | 0 | 1 | 0 |
ARID1A WILD-TYPE | 16 | 15 | 17 | 10 | 5 |
P value = 0.171 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 16 | 14 | 23 |
ARID1A MUTATED | 2 | 1 | 0 |
ARID1A WILD-TYPE | 14 | 13 | 23 |
P value = 0.532 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 20 | 9 | 14 | 2 | 8 |
ARID1A MUTATED | 2 | 0 | 0 | 0 | 1 |
ARID1A WILD-TYPE | 18 | 9 | 14 | 2 | 7 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 1 | 4 | 2 | 61 |
ARID1A MUTATED | 0 | 0 | 0 | 5 |
ARID1A WILD-TYPE | 1 | 4 | 2 | 56 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|
ALL | 1 | 38 | 29 |
ARID1A MUTATED | 0 | 3 | 2 |
ARID1A WILD-TYPE | 1 | 35 | 27 |
P value = 0.314 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|
ALL | 2 | 3 | 6 | 54 |
ARID1A MUTATED | 0 | 1 | 0 | 3 |
ARID1A WILD-TYPE | 2 | 2 | 6 | 51 |
P value = 0.256 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 9 | 3 | 53 |
ARID1A MUTATED | 0 | 1 | 3 |
ARID1A WILD-TYPE | 9 | 2 | 50 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 21 | 19 |
RBM10 MUTATED | 2 | 1 | 1 |
RBM10 WILD-TYPE | 22 | 20 | 18 |
P value = 0.789 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2 |
RBM10 MUTATED | 1 | 1 | 0 | 1 | 0 | 1 | 0 | 0 |
RBM10 WILD-TYPE | 5 | 11 | 12 | 8 | 6 | 8 | 8 | 2 |
P value = 0.469 (Fisher's exact test), Q value = 1
nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|
ALL | 17 | 18 | 17 | 11 | 5 |
RBM10 MUTATED | 1 | 1 | 0 | 1 | 1 |
RBM10 WILD-TYPE | 16 | 17 | 17 | 10 | 4 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 16 | 14 | 23 |
RBM10 MUTATED | 1 | 1 | 1 |
RBM10 WILD-TYPE | 15 | 13 | 22 |
P value = 0.78 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 20 | 9 | 14 | 2 | 8 |
RBM10 MUTATED | 1 | 0 | 1 | 0 | 1 |
RBM10 WILD-TYPE | 19 | 9 | 13 | 2 | 7 |
P value = 0.0164 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 1 | 4 | 2 | 61 |
RBM10 MUTATED | 0 | 2 | 0 | 1 |
RBM10 WILD-TYPE | 1 | 2 | 2 | 60 |
P value = 0.0443 (Fisher's exact test), Q value = 1
nPatients | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|
ALL | 1 | 38 | 29 |
RBM10 MUTATED | 1 | 1 | 1 |
RBM10 WILD-TYPE | 0 | 37 | 28 |
P value = 0.533 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|
ALL | 2 | 3 | 6 | 54 |
RBM10 MUTATED | 0 | 0 | 1 | 3 |
RBM10 WILD-TYPE | 2 | 3 | 5 | 51 |
P value = 0.566 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 9 | 3 | 53 |
RBM10 MUTATED | 1 | 0 | 3 |
RBM10 WILD-TYPE | 8 | 3 | 50 |
P value = 0.78 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 21 | 19 |
TCF7L2 MUTATED | 2 | 2 | 3 |
TCF7L2 WILD-TYPE | 22 | 19 | 16 |
P value = 0.204 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2 |
TCF7L2 MUTATED | 1 | 0 | 1 | 1 | 1 | 0 | 3 | 0 |
TCF7L2 WILD-TYPE | 5 | 12 | 11 | 8 | 5 | 9 | 5 | 2 |
P value = 0.227 (Fisher's exact test), Q value = 1
nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|
ALL | 17 | 18 | 17 | 11 | 5 |
TCF7L2 MUTATED | 4 | 0 | 2 | 1 | 0 |
TCF7L2 WILD-TYPE | 13 | 18 | 15 | 10 | 5 |
P value = 0.15 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 16 | 14 | 23 |
TCF7L2 MUTATED | 2 | 2 | 0 |
TCF7L2 WILD-TYPE | 14 | 12 | 23 |
P value = 0.292 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 20 | 9 | 14 | 2 | 8 |
TCF7L2 MUTATED | 2 | 0 | 0 | 0 | 2 |
TCF7L2 WILD-TYPE | 18 | 9 | 14 | 2 | 6 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 1 | 4 | 2 | 61 |
TCF7L2 MUTATED | 0 | 0 | 0 | 7 |
TCF7L2 WILD-TYPE | 1 | 4 | 2 | 54 |
P value = 0.306 (Fisher's exact test), Q value = 1
nPatients | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|
ALL | 1 | 38 | 29 |
TCF7L2 MUTATED | 0 | 2 | 5 |
TCF7L2 WILD-TYPE | 1 | 36 | 24 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|
ALL | 2 | 3 | 6 | 54 |
TCF7L2 MUTATED | 0 | 0 | 0 | 6 |
TCF7L2 WILD-TYPE | 2 | 3 | 6 | 48 |
P value = 0.69 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 9 | 3 | 53 |
TCF7L2 MUTATED | 0 | 0 | 6 |
TCF7L2 WILD-TYPE | 9 | 3 | 47 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 21 | 19 |
ERBB2 MUTATED | 2 | 1 | 1 |
ERBB2 WILD-TYPE | 22 | 20 | 18 |
P value = 0.877 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2 |
ERBB2 MUTATED | 0 | 1 | 2 | 1 | 0 | 0 | 0 | 0 |
ERBB2 WILD-TYPE | 6 | 11 | 10 | 8 | 6 | 9 | 8 | 2 |
P value = 0.469 (Fisher's exact test), Q value = 1
nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|
ALL | 17 | 18 | 17 | 11 | 5 |
ERBB2 MUTATED | 1 | 1 | 0 | 1 | 1 |
ERBB2 WILD-TYPE | 16 | 17 | 17 | 10 | 4 |
P value = 0.675 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 16 | 14 | 23 |
ERBB2 MUTATED | 1 | 2 | 1 |
ERBB2 WILD-TYPE | 15 | 12 | 22 |
P value = 0.409 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 20 | 9 | 14 | 2 | 8 |
ERBB2 MUTATED | 1 | 0 | 1 | 0 | 2 |
ERBB2 WILD-TYPE | 19 | 9 | 13 | 2 | 6 |
P value = 0.0308 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 1 | 4 | 2 | 61 |
ERBB2 MUTATED | 0 | 2 | 0 | 2 |
ERBB2 WILD-TYPE | 1 | 2 | 2 | 59 |
P value = 0.0349 (Fisher's exact test), Q value = 1
nPatients | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|
ALL | 1 | 38 | 29 |
ERBB2 MUTATED | 1 | 1 | 2 |
ERBB2 WILD-TYPE | 0 | 37 | 27 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|
ALL | 2 | 3 | 6 | 54 |
ERBB2 MUTATED | 0 | 0 | 0 | 3 |
ERBB2 WILD-TYPE | 2 | 3 | 6 | 51 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 9 | 3 | 53 |
ERBB2 MUTATED | 0 | 0 | 3 |
ERBB2 WILD-TYPE | 9 | 3 | 50 |
P value = 0.512 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 21 | 19 |
KIAA1804 MUTATED | 3 | 4 | 1 |
KIAA1804 WILD-TYPE | 21 | 17 | 18 |
P value = 0.837 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2 |
KIAA1804 MUTATED | 0 | 1 | 3 | 1 | 0 | 2 | 1 | 0 |
KIAA1804 WILD-TYPE | 6 | 11 | 9 | 8 | 6 | 7 | 7 | 2 |
P value = 0.474 (Fisher's exact test), Q value = 1
nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|
ALL | 17 | 18 | 17 | 11 | 5 |
KIAA1804 MUTATED | 2 | 4 | 3 | 0 | 0 |
KIAA1804 WILD-TYPE | 15 | 14 | 14 | 11 | 5 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 16 | 14 | 23 |
KIAA1804 MUTATED | 2 | 2 | 4 |
KIAA1804 WILD-TYPE | 14 | 12 | 19 |
P value = 0.599 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 20 | 9 | 14 | 2 | 8 |
KIAA1804 MUTATED | 3 | 0 | 3 | 0 | 2 |
KIAA1804 WILD-TYPE | 17 | 9 | 11 | 2 | 6 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 1 | 4 | 2 | 61 |
KIAA1804 MUTATED | 0 | 0 | 0 | 9 |
KIAA1804 WILD-TYPE | 1 | 4 | 2 | 52 |
P value = 0.758 (Fisher's exact test), Q value = 1
nPatients | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|
ALL | 1 | 38 | 29 |
KIAA1804 MUTATED | 0 | 6 | 3 |
KIAA1804 WILD-TYPE | 1 | 32 | 26 |
P value = 0.804 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|
ALL | 2 | 3 | 6 | 54 |
KIAA1804 MUTATED | 0 | 0 | 0 | 9 |
KIAA1804 WILD-TYPE | 2 | 3 | 6 | 45 |
P value = 0.574 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 9 | 3 | 53 |
KIAA1804 MUTATED | 0 | 0 | 9 |
KIAA1804 WILD-TYPE | 9 | 3 | 44 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 1 | 4 | 2 | 61 |
CCDC88C MUTATED | 0 | 0 | 0 | 3 |
CCDC88C WILD-TYPE | 1 | 4 | 2 | 58 |
P value = 0.593 (Fisher's exact test), Q value = 1
nPatients | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|
ALL | 1 | 38 | 29 |
CCDC88C MUTATED | 0 | 1 | 2 |
CCDC88C WILD-TYPE | 1 | 37 | 27 |
P value = 0.432 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|
ALL | 2 | 3 | 6 | 54 |
CCDC88C MUTATED | 0 | 0 | 1 | 2 |
CCDC88C WILD-TYPE | 2 | 3 | 5 | 52 |
P value = 0.466 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 9 | 3 | 53 |
CCDC88C MUTATED | 1 | 0 | 2 |
CCDC88C WILD-TYPE | 8 | 3 | 51 |
-
Mutation data file = transformed.cor.cli.txt
-
Molecular subtypes file = READ-TP.transferedmergedcluster.txt
-
Number of patients = 69
-
Number of significantly mutated genes = 12
-
Number of Molecular subtypes = 9
-
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.