This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 13 genes and 8 molecular subtypes across 57 patients, 2 significant findings detected with P value < 0.05 and Q value < 0.25.
-
PTEN mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
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 | |
PTEN | 11 (19%) | 46 |
0.011 (1.00) |
0.00012 (0.0125) |
0.00231 (0.238) |
0.0452 (1.00) |
0.0964 (1.00) |
0.0612 (1.00) |
0.0223 (1.00) |
0.122 (1.00) |
TP53 | 51 (89%) | 6 |
0.331 (1.00) |
0.627 (1.00) |
0.877 (1.00) |
0.513 (1.00) |
1 (1.00) |
0.911 (1.00) |
1 (1.00) |
1 (1.00) |
FBXW7 | 22 (39%) | 35 |
0.0631 (1.00) |
0.723 (1.00) |
0.633 (1.00) |
0.102 (1.00) |
0.47 (1.00) |
0.931 (1.00) |
0.975 (1.00) |
0.712 (1.00) |
PPP2R1A | 16 (28%) | 41 |
1 (1.00) |
0.709 (1.00) |
0.592 (1.00) |
0.673 (1.00) |
0.57 (1.00) |
0.318 (1.00) |
0.237 (1.00) |
0.49 (1.00) |
KRAS | 7 (12%) | 50 |
0.321 (1.00) |
0.0148 (1.00) |
0.0325 (1.00) |
0.00609 (0.615) |
0.462 (1.00) |
0.0906 (1.00) |
0.513 (1.00) |
0.0479 (1.00) |
ZBTB7B | 6 (11%) | 51 |
0.483 (1.00) |
0.94 (1.00) |
1 (1.00) |
0.913 (1.00) |
0.0995 (1.00) |
0.146 (1.00) |
0.15 (1.00) |
0.303 (1.00) |
CHD4 | 10 (18%) | 47 |
0.199 (1.00) |
0.0101 (1.00) |
0.187 (1.00) |
0.00576 (0.588) |
0.479 (1.00) |
0.412 (1.00) |
0.493 (1.00) |
0.479 (1.00) |
PIK3R1 | 6 (11%) | 51 |
0.855 (1.00) |
0.939 (1.00) |
0.546 (1.00) |
0.705 (1.00) |
0.426 (1.00) |
0.506 (1.00) |
0.743 (1.00) |
0.747 (1.00) |
ARHGAP35 | 6 (11%) | 51 |
1 (1.00) |
0.333 (1.00) |
1 (1.00) |
0.401 (1.00) |
1 (1.00) |
0.188 (1.00) |
1 (1.00) |
0.253 (1.00) |
PIK3CA | 20 (35%) | 37 |
0.256 (1.00) |
0.9 (1.00) |
0.365 (1.00) |
0.37 (1.00) |
0.111 (1.00) |
0.34 (1.00) |
0.165 (1.00) |
0.111 (1.00) |
MAMLD1 | 4 (7%) | 53 |
0.826 (1.00) |
0.9 (1.00) |
0.687 (1.00) |
0.769 (1.00) |
0.0638 (1.00) |
0.679 (1.00) |
0.163 (1.00) |
0.572 (1.00) |
RB1 | 6 (11%) | 51 |
0.544 (1.00) |
0.0894 (1.00) |
0.0783 (1.00) |
0.0981 (1.00) |
0.835 (1.00) |
0.862 (1.00) |
0.92 (1.00) |
0.688 (1.00) |
LYPLA2 | 3 (5%) | 54 |
1 (1.00) |
0.621 (1.00) |
0.673 (1.00) |
0.349 (1.00) |
0.381 (1.00) |
0.564 (1.00) |
0.478 (1.00) |
0.49 (1.00) |
P value = 0.331 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 24 | 10 |
TP53 MUTATED | 21 | 21 | 8 |
TP53 WILD-TYPE | 1 | 3 | 2 |
P value = 0.627 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 12 | 9 | 10 | 13 | 13 |
TP53 MUTATED | 12 | 8 | 8 | 12 | 11 |
TP53 WILD-TYPE | 0 | 1 | 2 | 1 | 2 |
P value = 0.877 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 20 | 12 | 10 |
TP53 MUTATED | 14 | 18 | 10 | 9 |
TP53 WILD-TYPE | 1 | 2 | 2 | 1 |
P value = 0.513 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14 |
TP53 MUTATED | 11 | 3 | 8 | 5 | 7 | 5 | 12 |
TP53 WILD-TYPE | 0 | 1 | 0 | 1 | 1 | 1 | 2 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 22 | 4 | 19 |
TP53 MUTATED | 10 | 20 | 4 | 17 |
TP53 WILD-TYPE | 1 | 2 | 0 | 2 |
P value = 0.911 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 8 | 18 | 6 |
TP53 MUTATED | 21 | 8 | 16 | 6 |
TP53 WILD-TYPE | 3 | 0 | 2 | 0 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 23 | 5 | 17 |
TP53 MUTATED | 10 | 21 | 5 | 15 |
TP53 WILD-TYPE | 1 | 2 | 0 | 2 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 7 | 15 | 10 | 9 | 5 |
TP53 MUTATED | 9 | 7 | 13 | 9 | 8 | 5 |
TP53 WILD-TYPE | 1 | 0 | 2 | 1 | 1 | 0 |
P value = 0.0631 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 24 | 10 |
FBXW7 MUTATED | 12 | 9 | 1 |
FBXW7 WILD-TYPE | 10 | 15 | 9 |
P value = 0.723 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 12 | 9 | 10 | 13 | 13 |
FBXW7 MUTATED | 6 | 4 | 4 | 3 | 5 |
FBXW7 WILD-TYPE | 6 | 5 | 6 | 10 | 8 |
P value = 0.633 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 20 | 12 | 10 |
FBXW7 MUTATED | 7 | 8 | 5 | 2 |
FBXW7 WILD-TYPE | 8 | 12 | 7 | 8 |
P value = 0.102 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14 |
FBXW7 MUTATED | 4 | 4 | 5 | 2 | 2 | 2 | 3 |
FBXW7 WILD-TYPE | 7 | 0 | 3 | 4 | 6 | 4 | 11 |
P value = 0.47 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 22 | 4 | 19 |
FBXW7 MUTATED | 5 | 8 | 3 | 6 |
FBXW7 WILD-TYPE | 6 | 14 | 1 | 13 |
P value = 0.931 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 8 | 18 | 6 |
FBXW7 MUTATED | 9 | 4 | 7 | 2 |
FBXW7 WILD-TYPE | 15 | 4 | 11 | 4 |
P value = 0.975 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 23 | 5 | 17 |
FBXW7 MUTATED | 5 | 9 | 2 | 6 |
FBXW7 WILD-TYPE | 6 | 14 | 3 | 11 |
P value = 0.712 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 7 | 15 | 10 | 9 | 5 |
FBXW7 MUTATED | 2 | 4 | 7 | 4 | 3 | 2 |
FBXW7 WILD-TYPE | 8 | 3 | 8 | 6 | 6 | 3 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 24 | 10 |
PPP2R1A MUTATED | 6 | 7 | 3 |
PPP2R1A WILD-TYPE | 16 | 17 | 7 |
P value = 0.709 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 12 | 9 | 10 | 13 | 13 |
PPP2R1A MUTATED | 4 | 3 | 4 | 3 | 2 |
PPP2R1A WILD-TYPE | 8 | 6 | 6 | 10 | 11 |
P value = 0.592 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 20 | 12 | 10 |
PPP2R1A MUTATED | 6 | 5 | 2 | 3 |
PPP2R1A WILD-TYPE | 9 | 15 | 10 | 7 |
P value = 0.673 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14 |
PPP2R1A MUTATED | 4 | 1 | 4 | 1 | 2 | 2 | 2 |
PPP2R1A WILD-TYPE | 7 | 3 | 4 | 5 | 6 | 4 | 12 |
P value = 0.57 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 22 | 4 | 19 |
PPP2R1A MUTATED | 5 | 5 | 1 | 5 |
PPP2R1A WILD-TYPE | 6 | 17 | 3 | 14 |
P value = 0.318 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 8 | 18 | 6 |
PPP2R1A MUTATED | 8 | 4 | 3 | 1 |
PPP2R1A WILD-TYPE | 16 | 4 | 15 | 5 |
P value = 0.237 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 23 | 5 | 17 |
PPP2R1A MUTATED | 6 | 5 | 1 | 4 |
PPP2R1A WILD-TYPE | 5 | 18 | 4 | 13 |
P value = 0.49 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 7 | 15 | 10 | 9 | 5 |
PPP2R1A MUTATED | 3 | 4 | 5 | 2 | 1 | 1 |
PPP2R1A WILD-TYPE | 7 | 3 | 10 | 8 | 8 | 4 |
P value = 0.011 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 24 | 10 |
PTEN MUTATED | 1 | 9 | 1 |
PTEN WILD-TYPE | 21 | 15 | 9 |
P value = 0.00012 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 12 | 9 | 10 | 13 | 13 |
PTEN MUTATED | 0 | 0 | 6 | 5 | 0 |
PTEN WILD-TYPE | 12 | 9 | 4 | 8 | 13 |
P value = 0.00231 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 20 | 12 | 10 |
PTEN MUTATED | 0 | 8 | 0 | 3 |
PTEN WILD-TYPE | 15 | 12 | 12 | 7 |
P value = 0.0452 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14 |
PTEN MUTATED | 0 | 0 | 3 | 0 | 3 | 0 | 5 |
PTEN WILD-TYPE | 11 | 4 | 5 | 6 | 5 | 6 | 9 |
P value = 0.0964 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 22 | 4 | 19 |
PTEN MUTATED | 2 | 1 | 1 | 6 |
PTEN WILD-TYPE | 9 | 21 | 3 | 13 |
P value = 0.0612 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 8 | 18 | 6 |
PTEN MUTATED | 8 | 0 | 1 | 1 |
PTEN WILD-TYPE | 16 | 8 | 17 | 5 |
P value = 0.0223 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 23 | 5 | 17 |
PTEN MUTATED | 1 | 1 | 2 | 6 |
PTEN WILD-TYPE | 10 | 22 | 3 | 11 |
P value = 0.122 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 7 | 15 | 10 | 9 | 5 |
PTEN MUTATED | 2 | 0 | 6 | 1 | 0 | 1 |
PTEN WILD-TYPE | 8 | 7 | 9 | 9 | 9 | 4 |
P value = 0.321 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 24 | 10 |
KRAS MUTATED | 2 | 5 | 0 |
KRAS WILD-TYPE | 20 | 19 | 10 |
P value = 0.0148 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 12 | 9 | 10 | 13 | 13 |
KRAS MUTATED | 0 | 1 | 1 | 0 | 5 |
KRAS WILD-TYPE | 12 | 8 | 9 | 13 | 8 |
P value = 0.0325 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 20 | 12 | 10 |
KRAS MUTATED | 0 | 3 | 4 | 0 |
KRAS WILD-TYPE | 15 | 17 | 8 | 10 |
P value = 0.00609 (Fisher's exact test), Q value = 0.62
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14 |
KRAS MUTATED | 0 | 0 | 1 | 0 | 0 | 4 | 2 |
KRAS WILD-TYPE | 11 | 4 | 7 | 6 | 8 | 2 | 12 |
P value = 0.462 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 22 | 4 | 19 |
KRAS MUTATED | 1 | 4 | 1 | 1 |
KRAS WILD-TYPE | 10 | 18 | 3 | 18 |
P value = 0.0906 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 8 | 18 | 6 |
KRAS MUTATED | 1 | 0 | 5 | 1 |
KRAS WILD-TYPE | 23 | 8 | 13 | 5 |
P value = 0.513 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 23 | 5 | 17 |
KRAS MUTATED | 1 | 5 | 0 | 1 |
KRAS WILD-TYPE | 10 | 18 | 5 | 16 |
P value = 0.0479 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 7 | 15 | 10 | 9 | 5 |
KRAS MUTATED | 0 | 0 | 1 | 1 | 4 | 1 |
KRAS WILD-TYPE | 10 | 7 | 14 | 9 | 5 | 4 |
P value = 0.483 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 24 | 10 |
ZBTB7B MUTATED | 3 | 1 | 1 |
ZBTB7B WILD-TYPE | 19 | 23 | 9 |
P value = 0.94 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 12 | 9 | 10 | 13 | 13 |
ZBTB7B MUTATED | 2 | 1 | 1 | 1 | 1 |
ZBTB7B WILD-TYPE | 10 | 8 | 9 | 12 | 12 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 20 | 12 | 10 |
ZBTB7B MUTATED | 2 | 2 | 1 | 1 |
ZBTB7B WILD-TYPE | 13 | 18 | 11 | 9 |
P value = 0.913 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14 |
ZBTB7B MUTATED | 2 | 0 | 0 | 0 | 1 | 1 | 2 |
ZBTB7B WILD-TYPE | 9 | 4 | 8 | 6 | 7 | 5 | 12 |
P value = 0.0995 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 22 | 4 | 19 |
ZBTB7B MUTATED | 1 | 1 | 2 | 2 |
ZBTB7B WILD-TYPE | 10 | 21 | 2 | 17 |
P value = 0.146 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 8 | 18 | 6 |
ZBTB7B MUTATED | 5 | 1 | 0 | 0 |
ZBTB7B WILD-TYPE | 19 | 7 | 18 | 6 |
P value = 0.15 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 23 | 5 | 17 |
ZBTB7B MUTATED | 1 | 1 | 2 | 2 |
ZBTB7B WILD-TYPE | 10 | 22 | 3 | 15 |
P value = 0.303 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 7 | 15 | 10 | 9 | 5 |
ZBTB7B MUTATED | 1 | 1 | 4 | 0 | 0 | 0 |
ZBTB7B WILD-TYPE | 9 | 6 | 11 | 10 | 9 | 5 |
P value = 0.199 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 24 | 10 |
CHD4 MUTATED | 2 | 7 | 1 |
CHD4 WILD-TYPE | 20 | 17 | 9 |
P value = 0.0101 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 12 | 9 | 10 | 13 | 13 |
CHD4 MUTATED | 0 | 4 | 4 | 1 | 1 |
CHD4 WILD-TYPE | 12 | 5 | 6 | 12 | 12 |
P value = 0.187 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 20 | 12 | 10 |
CHD4 MUTATED | 2 | 5 | 0 | 3 |
CHD4 WILD-TYPE | 13 | 15 | 12 | 7 |
P value = 0.00576 (Fisher's exact test), Q value = 0.59
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14 |
CHD4 MUTATED | 0 | 2 | 4 | 0 | 3 | 0 | 1 |
CHD4 WILD-TYPE | 11 | 2 | 4 | 6 | 5 | 6 | 13 |
P value = 0.479 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 22 | 4 | 19 |
CHD4 MUTATED | 3 | 2 | 1 | 3 |
CHD4 WILD-TYPE | 8 | 20 | 3 | 16 |
P value = 0.412 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 8 | 18 | 6 |
CHD4 MUTATED | 6 | 0 | 2 | 1 |
CHD4 WILD-TYPE | 18 | 8 | 16 | 5 |
P value = 0.493 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 23 | 5 | 17 |
CHD4 MUTATED | 3 | 2 | 1 | 3 |
CHD4 WILD-TYPE | 8 | 21 | 4 | 14 |
P value = 0.479 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 7 | 15 | 10 | 9 | 5 |
CHD4 MUTATED | 2 | 0 | 4 | 2 | 0 | 1 |
CHD4 WILD-TYPE | 8 | 7 | 11 | 8 | 9 | 4 |
P value = 0.855 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 24 | 10 |
PIK3R1 MUTATED | 3 | 2 | 1 |
PIK3R1 WILD-TYPE | 19 | 22 | 9 |
P value = 0.939 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 12 | 9 | 10 | 13 | 13 |
PIK3R1 MUTATED | 2 | 1 | 1 | 1 | 1 |
PIK3R1 WILD-TYPE | 10 | 8 | 9 | 12 | 12 |
P value = 0.546 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 20 | 12 | 10 |
PIK3R1 MUTATED | 3 | 2 | 1 | 0 |
PIK3R1 WILD-TYPE | 12 | 18 | 11 | 10 |
P value = 0.705 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14 |
PIK3R1 MUTATED | 2 | 1 | 1 | 0 | 0 | 1 | 1 |
PIK3R1 WILD-TYPE | 9 | 3 | 7 | 6 | 8 | 5 | 13 |
P value = 0.426 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 22 | 4 | 19 |
PIK3R1 MUTATED | 2 | 2 | 1 | 1 |
PIK3R1 WILD-TYPE | 9 | 20 | 3 | 18 |
P value = 0.506 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 8 | 18 | 6 |
PIK3R1 MUTATED | 2 | 2 | 2 | 0 |
PIK3R1 WILD-TYPE | 22 | 6 | 16 | 6 |
P value = 0.743 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 23 | 5 | 17 |
PIK3R1 MUTATED | 2 | 3 | 0 | 1 |
PIK3R1 WILD-TYPE | 9 | 20 | 5 | 16 |
P value = 0.747 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 7 | 15 | 10 | 9 | 5 |
PIK3R1 MUTATED | 1 | 2 | 1 | 1 | 1 | 0 |
PIK3R1 WILD-TYPE | 9 | 5 | 14 | 9 | 8 | 5 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 24 | 10 |
ARHGAP35 MUTATED | 2 | 3 | 1 |
ARHGAP35 WILD-TYPE | 20 | 21 | 9 |
P value = 0.333 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 12 | 9 | 10 | 13 | 13 |
ARHGAP35 MUTATED | 2 | 0 | 2 | 0 | 2 |
ARHGAP35 WILD-TYPE | 10 | 9 | 8 | 13 | 11 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 20 | 12 | 10 |
ARHGAP35 MUTATED | 2 | 2 | 1 | 1 |
ARHGAP35 WILD-TYPE | 13 | 18 | 11 | 9 |
P value = 0.401 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14 |
ARHGAP35 MUTATED | 2 | 0 | 2 | 0 | 1 | 1 | 0 |
ARHGAP35 WILD-TYPE | 9 | 4 | 6 | 6 | 7 | 5 | 14 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 22 | 4 | 19 |
ARHGAP35 MUTATED | 1 | 2 | 0 | 2 |
ARHGAP35 WILD-TYPE | 10 | 20 | 4 | 17 |
P value = 0.188 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 8 | 18 | 6 |
ARHGAP35 MUTATED | 1 | 2 | 1 | 1 |
ARHGAP35 WILD-TYPE | 23 | 6 | 17 | 5 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 23 | 5 | 17 |
ARHGAP35 MUTATED | 1 | 2 | 0 | 2 |
ARHGAP35 WILD-TYPE | 10 | 21 | 5 | 15 |
P value = 0.253 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 7 | 15 | 10 | 9 | 5 |
ARHGAP35 MUTATED | 0 | 2 | 1 | 1 | 0 | 1 |
ARHGAP35 WILD-TYPE | 10 | 5 | 14 | 9 | 9 | 4 |
P value = 0.256 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 24 | 10 |
PIK3CA MUTATED | 5 | 11 | 3 |
PIK3CA WILD-TYPE | 17 | 13 | 7 |
P value = 0.9 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 12 | 9 | 10 | 13 | 13 |
PIK3CA MUTATED | 4 | 3 | 5 | 4 | 4 |
PIK3CA WILD-TYPE | 8 | 6 | 5 | 9 | 9 |
P value = 0.365 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 20 | 12 | 10 |
PIK3CA MUTATED | 5 | 10 | 3 | 2 |
PIK3CA WILD-TYPE | 10 | 10 | 9 | 8 |
P value = 0.37 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14 |
PIK3CA MUTATED | 3 | 3 | 4 | 2 | 1 | 1 | 6 |
PIK3CA WILD-TYPE | 8 | 1 | 4 | 4 | 7 | 5 | 8 |
P value = 0.111 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 22 | 4 | 19 |
PIK3CA MUTATED | 4 | 4 | 2 | 10 |
PIK3CA WILD-TYPE | 7 | 18 | 2 | 9 |
P value = 0.34 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 8 | 18 | 6 |
PIK3CA MUTATED | 11 | 2 | 4 | 3 |
PIK3CA WILD-TYPE | 13 | 6 | 14 | 3 |
P value = 0.165 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 23 | 5 | 17 |
PIK3CA MUTATED | 5 | 5 | 1 | 9 |
PIK3CA WILD-TYPE | 6 | 18 | 4 | 8 |
P value = 0.111 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 7 | 15 | 10 | 9 | 5 |
PIK3CA MUTATED | 3 | 1 | 9 | 3 | 1 | 3 |
PIK3CA WILD-TYPE | 7 | 6 | 6 | 7 | 8 | 2 |
P value = 0.826 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 24 | 10 |
MAMLD1 MUTATED | 1 | 2 | 1 |
MAMLD1 WILD-TYPE | 21 | 22 | 9 |
P value = 0.9 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 12 | 9 | 10 | 13 | 13 |
MAMLD1 MUTATED | 0 | 1 | 1 | 1 | 1 |
MAMLD1 WILD-TYPE | 12 | 8 | 9 | 12 | 12 |
P value = 0.687 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 20 | 12 | 10 |
MAMLD1 MUTATED | 0 | 2 | 1 | 1 |
MAMLD1 WILD-TYPE | 15 | 18 | 11 | 9 |
P value = 0.769 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14 |
MAMLD1 MUTATED | 0 | 0 | 1 | 1 | 1 | 0 | 1 |
MAMLD1 WILD-TYPE | 11 | 4 | 7 | 5 | 7 | 6 | 13 |
P value = 0.0638 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 22 | 4 | 19 |
MAMLD1 MUTATED | 0 | 0 | 1 | 3 |
MAMLD1 WILD-TYPE | 11 | 22 | 3 | 16 |
P value = 0.679 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 8 | 18 | 6 |
MAMLD1 MUTATED | 2 | 0 | 1 | 1 |
MAMLD1 WILD-TYPE | 22 | 8 | 17 | 5 |
P value = 0.163 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 23 | 5 | 17 |
MAMLD1 MUTATED | 1 | 0 | 1 | 2 |
MAMLD1 WILD-TYPE | 10 | 23 | 4 | 15 |
P value = 0.572 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 7 | 15 | 10 | 9 | 5 |
MAMLD1 MUTATED | 1 | 0 | 2 | 0 | 0 | 1 |
MAMLD1 WILD-TYPE | 9 | 7 | 13 | 10 | 9 | 4 |
P value = 0.544 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 24 | 10 |
RB1 MUTATED | 2 | 4 | 0 |
RB1 WILD-TYPE | 20 | 20 | 10 |
P value = 0.0894 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 12 | 9 | 10 | 13 | 13 |
RB1 MUTATED | 0 | 1 | 3 | 2 | 0 |
RB1 WILD-TYPE | 12 | 8 | 7 | 11 | 13 |
P value = 0.0783 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 20 | 12 | 10 |
RB1 MUTATED | 0 | 4 | 0 | 2 |
RB1 WILD-TYPE | 15 | 16 | 12 | 8 |
P value = 0.0981 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14 |
RB1 MUTATED | 0 | 0 | 2 | 0 | 3 | 0 | 1 |
RB1 WILD-TYPE | 11 | 4 | 6 | 6 | 5 | 6 | 13 |
P value = 0.835 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 22 | 4 | 19 |
RB1 MUTATED | 2 | 2 | 0 | 2 |
RB1 WILD-TYPE | 9 | 20 | 4 | 17 |
P value = 0.862 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 8 | 18 | 6 |
RB1 MUTATED | 3 | 0 | 2 | 1 |
RB1 WILD-TYPE | 21 | 8 | 16 | 5 |
P value = 0.92 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 23 | 5 | 17 |
RB1 MUTATED | 1 | 2 | 1 | 2 |
RB1 WILD-TYPE | 10 | 21 | 4 | 15 |
P value = 0.688 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 7 | 15 | 10 | 9 | 5 |
RB1 MUTATED | 1 | 0 | 2 | 2 | 0 | 1 |
RB1 WILD-TYPE | 9 | 7 | 13 | 8 | 9 | 4 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 24 | 10 |
LYPLA2 MUTATED | 1 | 2 | 0 |
LYPLA2 WILD-TYPE | 21 | 22 | 10 |
P value = 0.621 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 12 | 9 | 10 | 13 | 13 |
LYPLA2 MUTATED | 0 | 1 | 1 | 0 | 1 |
LYPLA2 WILD-TYPE | 12 | 8 | 9 | 13 | 12 |
P value = 0.673 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 20 | 12 | 10 |
LYPLA2 MUTATED | 0 | 1 | 1 | 1 |
LYPLA2 WILD-TYPE | 15 | 19 | 11 | 9 |
P value = 0.349 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14 |
LYPLA2 MUTATED | 0 | 0 | 1 | 0 | 1 | 1 | 0 |
LYPLA2 WILD-TYPE | 11 | 4 | 7 | 6 | 7 | 5 | 14 |
P value = 0.381 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 22 | 4 | 19 |
LYPLA2 MUTATED | 0 | 1 | 1 | 1 |
LYPLA2 WILD-TYPE | 11 | 21 | 3 | 18 |
P value = 0.564 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 8 | 18 | 6 |
LYPLA2 MUTATED | 1 | 0 | 1 | 1 |
LYPLA2 WILD-TYPE | 23 | 8 | 17 | 5 |
P value = 0.478 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 23 | 5 | 17 |
LYPLA2 MUTATED | 0 | 1 | 1 | 1 |
LYPLA2 WILD-TYPE | 11 | 22 | 4 | 16 |
P value = 0.49 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 7 | 15 | 10 | 9 | 5 |
LYPLA2 MUTATED | 0 | 0 | 1 | 0 | 1 | 1 |
LYPLA2 WILD-TYPE | 10 | 7 | 14 | 10 | 8 | 4 |
-
Mutation data file = transformed.cor.cli.txt
-
Molecular subtypes file = UCS-TP.transferedmergedcluster.txt
-
Number of patients = 57
-
Number of significantly mutated genes = 13
-
Number of Molecular subtypes = 8
-
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.