This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 8 genes and 10 molecular subtypes across 66 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.
-
No gene mutations related to molecuar subtypes.
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 | |
TP53 | 22 (33%) | 44 |
0.361 (1.00) |
0.0876 (0.67) |
0.168 (1.00) |
0.0551 (0.67) |
0.0512 (0.67) |
0.0152 (0.464) |
0.949 (1.00) |
0.662 (1.00) |
0.764 (1.00) |
0.607 (1.00) |
PTEN | 6 (9%) | 60 |
0.735 (1.00) |
0.228 (1.00) |
0.309 (1.00) |
0.848 (1.00) |
0.428 (1.00) |
0.477 (1.00) |
0.559 (1.00) |
0.0683 (0.67) |
0.00401 (0.321) |
0.0174 (0.464) |
ZNF814 | 3 (5%) | 63 |
0.602 (1.00) |
0.1 (0.67) |
1 (1.00) |
1 (1.00) |
0.0611 (0.67) |
0.0772 (0.67) |
0.233 (1.00) |
0.281 (1.00) |
||
CDC27 | 6 (9%) | 60 |
1 (1.00) |
1 (1.00) |
0.558 (1.00) |
0.752 (1.00) |
0.196 (1.00) |
0.369 (1.00) |
0.734 (1.00) |
0.858 (1.00) |
0.826 (1.00) |
0.63 (1.00) |
PABPC1 | 7 (11%) | 59 |
1 (1.00) |
0.536 (1.00) |
0.533 (1.00) |
0.666 (1.00) |
0.482 (1.00) |
0.742 (1.00) |
0.775 (1.00) |
0.308 (1.00) |
0.759 (1.00) |
0.284 (1.00) |
AMAC1L3 | 5 (8%) | 61 |
1 (1.00) |
0.214 (1.00) |
0.559 (1.00) |
0.81 (1.00) |
0.311 (1.00) |
0.0436 (0.67) |
0.383 (1.00) |
0.101 (0.67) |
1 (1.00) |
0.624 (1.00) |
GFM1 | 3 (5%) | 63 |
1 (1.00) |
0.782 (1.00) |
0.615 (1.00) |
0.594 (1.00) |
1 (1.00) |
1 (1.00) |
0.474 (1.00) |
0.606 (1.00) |
||
PABPC3 | 7 (11%) | 59 |
1 (1.00) |
0.613 (1.00) |
0.879 (1.00) |
0.212 (1.00) |
0.892 (1.00) |
0.71 (1.00) |
1 (1.00) |
0.293 (1.00) |
0.6 (1.00) |
0.602 (1.00) |
P value = 0.361 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 38 | 26 | 2 |
TP53 MUTATED | 11 | 11 | 0 |
TP53 WILD-TYPE | 27 | 15 | 2 |
P value = 0.0876 (Fisher's exact test), Q value = 0.67
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 19 | 29 | 18 |
TP53 MUTATED | 4 | 14 | 4 |
TP53 WILD-TYPE | 15 | 15 | 14 |
P value = 0.168 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 26 | 17 | 20 |
TP53 MUTATED | 12 | 6 | 4 |
TP53 WILD-TYPE | 14 | 11 | 16 |
P value = 0.0551 (Fisher's exact test), Q value = 0.67
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 29 | 20 | 14 |
TP53 MUTATED | 14 | 3 | 5 |
TP53 WILD-TYPE | 15 | 17 | 9 |
P value = 0.0512 (Fisher's exact test), Q value = 0.67
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 17 | 15 | 5 | 6 | 14 | 4 | 5 |
TP53 MUTATED | 4 | 6 | 1 | 0 | 9 | 0 | 2 |
TP53 WILD-TYPE | 13 | 9 | 4 | 6 | 5 | 4 | 3 |
P value = 0.0152 (Fisher's exact test), Q value = 0.46
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
TP53 MUTATED | 5 | 6 | 1 | 0 | 7 | 3 | 0 |
TP53 WILD-TYPE | 14 | 10 | 6 | 6 | 3 | 1 | 4 |
P value = 0.949 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 18 | 26 | 10 | 12 |
TP53 MUTATED | 5 | 9 | 4 | 4 |
TP53 WILD-TYPE | 13 | 17 | 6 | 8 |
P value = 0.662 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9 |
TP53 MUTATED | 7 | 5 | 3 | 1 | 1 | 3 | 2 |
TP53 WILD-TYPE | 11 | 6 | 9 | 5 | 4 | 2 | 7 |
P value = 0.764 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 9 | 13 | 14 | 12 |
TP53 MUTATED | 3 | 4 | 7 | 4 |
TP53 WILD-TYPE | 6 | 9 | 7 | 8 |
P value = 0.607 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 5 | 6 | 5 | 8 | 5 | 4 | 6 | 5 | 4 |
TP53 MUTATED | 1 | 3 | 3 | 2 | 2 | 1 | 3 | 3 | 0 |
TP53 WILD-TYPE | 4 | 3 | 2 | 6 | 3 | 3 | 3 | 2 | 4 |
P value = 0.735 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 38 | 26 | 2 |
PTEN MUTATED | 3 | 3 | 0 |
PTEN WILD-TYPE | 35 | 23 | 2 |
P value = 0.228 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 19 | 29 | 18 |
PTEN MUTATED | 3 | 3 | 0 |
PTEN WILD-TYPE | 16 | 26 | 18 |
P value = 0.309 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 26 | 17 | 20 |
PTEN MUTATED | 3 | 2 | 0 |
PTEN WILD-TYPE | 23 | 15 | 20 |
P value = 0.848 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 29 | 20 | 14 |
PTEN MUTATED | 3 | 1 | 1 |
PTEN WILD-TYPE | 26 | 19 | 13 |
P value = 0.428 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 17 | 15 | 5 | 6 | 14 | 4 | 5 |
PTEN MUTATED | 2 | 0 | 0 | 0 | 3 | 0 | 1 |
PTEN WILD-TYPE | 15 | 15 | 5 | 6 | 11 | 4 | 4 |
P value = 0.477 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
PTEN MUTATED | 2 | 1 | 0 | 0 | 3 | 0 | 0 |
PTEN WILD-TYPE | 17 | 15 | 7 | 6 | 7 | 4 | 4 |
P value = 0.559 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 18 | 26 | 10 | 12 |
PTEN MUTATED | 1 | 4 | 1 | 0 |
PTEN WILD-TYPE | 17 | 22 | 9 | 12 |
P value = 0.0683 (Fisher's exact test), Q value = 0.67
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9 |
PTEN MUTATED | 5 | 0 | 0 | 0 | 0 | 1 | 0 |
PTEN WILD-TYPE | 13 | 11 | 12 | 6 | 5 | 4 | 9 |
P value = 0.00401 (Fisher's exact test), Q value = 0.32
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 9 | 13 | 14 | 12 |
PTEN MUTATED | 4 | 0 | 1 | 0 |
PTEN WILD-TYPE | 5 | 13 | 13 | 12 |
P value = 0.0174 (Fisher's exact test), Q value = 0.46
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 5 | 6 | 5 | 8 | 5 | 4 | 6 | 5 | 4 |
PTEN MUTATED | 3 | 0 | 1 | 0 | 0 | 0 | 0 | 1 | 0 |
PTEN WILD-TYPE | 2 | 6 | 4 | 8 | 5 | 4 | 6 | 4 | 4 |
P value = 0.602 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 38 | 26 | 2 |
ZNF814 MUTATED | 1 | 2 | 0 |
ZNF814 WILD-TYPE | 37 | 24 | 2 |
P value = 0.1 (Fisher's exact test), Q value = 0.67
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 19 | 29 | 18 |
ZNF814 MUTATED | 1 | 0 | 2 |
ZNF814 WILD-TYPE | 18 | 29 | 16 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 26 | 17 | 20 |
ZNF814 MUTATED | 1 | 1 | 1 |
ZNF814 WILD-TYPE | 25 | 16 | 19 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 29 | 20 | 14 |
ZNF814 MUTATED | 1 | 1 | 1 |
ZNF814 WILD-TYPE | 28 | 19 | 13 |
P value = 0.0611 (Fisher's exact test), Q value = 0.67
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 17 | 15 | 5 | 6 | 14 | 4 | 5 |
ZNF814 MUTATED | 0 | 1 | 0 | 2 | 0 | 0 | 0 |
ZNF814 WILD-TYPE | 17 | 14 | 5 | 4 | 14 | 4 | 5 |
P value = 0.0772 (Fisher's exact test), Q value = 0.67
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
ZNF814 MUTATED | 0 | 1 | 0 | 2 | 0 | 0 | 0 |
ZNF814 WILD-TYPE | 19 | 15 | 7 | 4 | 10 | 4 | 4 |
P value = 0.233 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 18 | 26 | 10 | 12 |
ZNF814 MUTATED | 2 | 0 | 0 | 1 |
ZNF814 WILD-TYPE | 16 | 26 | 10 | 11 |
P value = 0.281 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9 |
ZNF814 MUTATED | 0 | 0 | 1 | 0 | 1 | 0 | 1 |
ZNF814 WILD-TYPE | 18 | 11 | 11 | 6 | 4 | 5 | 8 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 38 | 26 | 2 |
CDC27 MUTATED | 4 | 2 | 0 |
CDC27 WILD-TYPE | 34 | 24 | 2 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 19 | 29 | 18 |
CDC27 MUTATED | 2 | 3 | 1 |
CDC27 WILD-TYPE | 17 | 26 | 17 |
P value = 0.558 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 26 | 17 | 20 |
CDC27 MUTATED | 4 | 1 | 1 |
CDC27 WILD-TYPE | 22 | 16 | 19 |
P value = 0.752 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 29 | 20 | 14 |
CDC27 MUTATED | 4 | 1 | 1 |
CDC27 WILD-TYPE | 25 | 19 | 13 |
P value = 0.196 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 17 | 15 | 5 | 6 | 14 | 4 | 5 |
CDC27 MUTATED | 1 | 4 | 0 | 0 | 0 | 0 | 1 |
CDC27 WILD-TYPE | 16 | 11 | 5 | 6 | 14 | 4 | 4 |
P value = 0.369 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
CDC27 MUTATED | 1 | 4 | 1 | 0 | 0 | 0 | 0 |
CDC27 WILD-TYPE | 18 | 12 | 6 | 6 | 10 | 4 | 4 |
P value = 0.734 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 18 | 26 | 10 | 12 |
CDC27 MUTATED | 2 | 2 | 0 | 2 |
CDC27 WILD-TYPE | 16 | 24 | 10 | 10 |
P value = 0.858 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9 |
CDC27 MUTATED | 1 | 1 | 2 | 0 | 0 | 1 | 1 |
CDC27 WILD-TYPE | 17 | 10 | 10 | 6 | 5 | 4 | 8 |
P value = 0.826 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 9 | 13 | 14 | 12 |
CDC27 MUTATED | 0 | 2 | 1 | 1 |
CDC27 WILD-TYPE | 9 | 11 | 13 | 11 |
P value = 0.63 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 5 | 6 | 5 | 8 | 5 | 4 | 6 | 5 | 4 |
CDC27 MUTATED | 0 | 2 | 0 | 1 | 0 | 0 | 1 | 0 | 0 |
CDC27 WILD-TYPE | 5 | 4 | 5 | 7 | 5 | 4 | 5 | 5 | 4 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 38 | 26 | 2 |
PABPC1 MUTATED | 4 | 3 | 0 |
PABPC1 WILD-TYPE | 34 | 23 | 2 |
P value = 0.536 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 19 | 29 | 18 |
PABPC1 MUTATED | 2 | 2 | 3 |
PABPC1 WILD-TYPE | 17 | 27 | 15 |
P value = 0.533 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 26 | 17 | 20 |
PABPC1 MUTATED | 4 | 2 | 1 |
PABPC1 WILD-TYPE | 22 | 15 | 19 |
P value = 0.666 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 29 | 20 | 14 |
PABPC1 MUTATED | 4 | 1 | 2 |
PABPC1 WILD-TYPE | 25 | 19 | 12 |
P value = 0.482 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 17 | 15 | 5 | 6 | 14 | 4 | 5 |
PABPC1 MUTATED | 2 | 1 | 0 | 1 | 1 | 0 | 2 |
PABPC1 WILD-TYPE | 15 | 14 | 5 | 5 | 13 | 4 | 3 |
P value = 0.742 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
PABPC1 MUTATED | 2 | 1 | 2 | 1 | 1 | 0 | 0 |
PABPC1 WILD-TYPE | 17 | 15 | 5 | 5 | 9 | 4 | 4 |
P value = 0.775 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 18 | 26 | 10 | 12 |
PABPC1 MUTATED | 2 | 4 | 0 | 1 |
PABPC1 WILD-TYPE | 16 | 22 | 10 | 11 |
P value = 0.308 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9 |
PABPC1 MUTATED | 2 | 1 | 0 | 1 | 0 | 0 | 3 |
PABPC1 WILD-TYPE | 16 | 10 | 12 | 5 | 5 | 5 | 6 |
P value = 0.759 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 9 | 13 | 14 | 12 |
PABPC1 MUTATED | 0 | 1 | 1 | 2 |
PABPC1 WILD-TYPE | 9 | 12 | 13 | 10 |
P value = 0.284 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 5 | 6 | 5 | 8 | 5 | 4 | 6 | 5 | 4 |
PABPC1 MUTATED | 0 | 0 | 1 | 0 | 0 | 0 | 2 | 1 | 0 |
PABPC1 WILD-TYPE | 5 | 6 | 4 | 8 | 5 | 4 | 4 | 4 | 4 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 38 | 26 | 2 |
AMAC1L3 MUTATED | 3 | 2 | 0 |
AMAC1L3 WILD-TYPE | 35 | 24 | 2 |
P value = 0.214 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 19 | 29 | 18 |
AMAC1L3 MUTATED | 0 | 4 | 1 |
AMAC1L3 WILD-TYPE | 19 | 25 | 17 |
P value = 0.559 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 26 | 17 | 20 |
AMAC1L3 MUTATED | 2 | 0 | 2 |
AMAC1L3 WILD-TYPE | 24 | 17 | 18 |
P value = 0.81 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 29 | 20 | 14 |
AMAC1L3 MUTATED | 2 | 2 | 0 |
AMAC1L3 WILD-TYPE | 27 | 18 | 14 |
P value = 0.311 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 17 | 15 | 5 | 6 | 14 | 4 | 5 |
AMAC1L3 MUTATED | 0 | 1 | 0 | 1 | 3 | 0 | 0 |
AMAC1L3 WILD-TYPE | 17 | 14 | 5 | 5 | 11 | 4 | 5 |
P value = 0.0436 (Fisher's exact test), Q value = 0.67
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
AMAC1L3 MUTATED | 0 | 1 | 0 | 1 | 1 | 2 | 0 |
AMAC1L3 WILD-TYPE | 19 | 15 | 7 | 5 | 9 | 2 | 4 |
P value = 0.383 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 18 | 26 | 10 | 12 |
AMAC1L3 MUTATED | 2 | 1 | 0 | 2 |
AMAC1L3 WILD-TYPE | 16 | 25 | 10 | 10 |
P value = 0.101 (Fisher's exact test), Q value = 0.67
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9 |
AMAC1L3 MUTATED | 0 | 2 | 1 | 2 | 0 | 0 | 0 |
AMAC1L3 WILD-TYPE | 18 | 9 | 11 | 4 | 5 | 5 | 9 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 9 | 13 | 14 | 12 |
AMAC1L3 MUTATED | 0 | 1 | 1 | 1 |
AMAC1L3 WILD-TYPE | 9 | 12 | 13 | 11 |
P value = 0.624 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 5 | 6 | 5 | 8 | 5 | 4 | 6 | 5 | 4 |
AMAC1L3 MUTATED | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 1 | 0 |
AMAC1L3 WILD-TYPE | 5 | 6 | 4 | 8 | 5 | 4 | 5 | 4 | 4 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 38 | 26 | 2 |
GFM1 MUTATED | 2 | 1 | 0 |
GFM1 WILD-TYPE | 36 | 25 | 2 |
P value = 0.782 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 19 | 29 | 18 |
GFM1 MUTATED | 1 | 2 | 0 |
GFM1 WILD-TYPE | 18 | 27 | 18 |
P value = 0.615 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 26 | 17 | 20 |
GFM1 MUTATED | 2 | 1 | 0 |
GFM1 WILD-TYPE | 24 | 16 | 20 |
P value = 0.594 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 29 | 20 | 14 |
GFM1 MUTATED | 2 | 0 | 1 |
GFM1 WILD-TYPE | 27 | 20 | 13 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 17 | 15 | 5 | 6 | 14 | 4 | 5 |
GFM1 MUTATED | 1 | 1 | 0 | 0 | 1 | 0 | 0 |
GFM1 WILD-TYPE | 16 | 14 | 5 | 6 | 13 | 4 | 5 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
GFM1 MUTATED | 1 | 1 | 0 | 0 | 1 | 0 | 0 |
GFM1 WILD-TYPE | 18 | 15 | 7 | 6 | 9 | 4 | 4 |
P value = 0.474 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 18 | 26 | 10 | 12 |
GFM1 MUTATED | 0 | 2 | 1 | 0 |
GFM1 WILD-TYPE | 18 | 24 | 9 | 12 |
P value = 0.606 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9 |
GFM1 MUTATED | 1 | 1 | 0 | 0 | 0 | 1 | 0 |
GFM1 WILD-TYPE | 17 | 10 | 12 | 6 | 5 | 4 | 9 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 38 | 26 | 2 |
PABPC3 MUTATED | 4 | 3 | 0 |
PABPC3 WILD-TYPE | 34 | 23 | 2 |
P value = 0.613 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 19 | 29 | 18 |
PABPC3 MUTATED | 3 | 2 | 2 |
PABPC3 WILD-TYPE | 16 | 27 | 16 |
P value = 0.879 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 26 | 17 | 20 |
PABPC3 MUTATED | 3 | 1 | 3 |
PABPC3 WILD-TYPE | 23 | 16 | 17 |
P value = 0.212 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 29 | 20 | 14 |
PABPC3 MUTATED | 3 | 4 | 0 |
PABPC3 WILD-TYPE | 26 | 16 | 14 |
P value = 0.892 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 17 | 15 | 5 | 6 | 14 | 4 | 5 |
PABPC3 MUTATED | 3 | 2 | 0 | 0 | 1 | 0 | 1 |
PABPC3 WILD-TYPE | 14 | 13 | 5 | 6 | 13 | 4 | 4 |
P value = 0.71 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
PABPC3 MUTATED | 3 | 2 | 1 | 0 | 0 | 1 | 0 |
PABPC3 WILD-TYPE | 16 | 14 | 6 | 6 | 10 | 3 | 4 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 18 | 26 | 10 | 12 |
PABPC3 MUTATED | 2 | 3 | 1 | 1 |
PABPC3 WILD-TYPE | 16 | 23 | 9 | 11 |
P value = 0.293 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9 |
PABPC3 MUTATED | 3 | 1 | 0 | 0 | 2 | 0 | 1 |
PABPC3 WILD-TYPE | 15 | 10 | 12 | 6 | 3 | 5 | 8 |
P value = 0.6 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 9 | 13 | 14 | 12 |
PABPC3 MUTATED | 1 | 1 | 1 | 3 |
PABPC3 WILD-TYPE | 8 | 12 | 13 | 9 |
P value = 0.602 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 5 | 6 | 5 | 8 | 5 | 4 | 6 | 5 | 4 |
PABPC3 MUTATED | 0 | 0 | 2 | 1 | 0 | 1 | 1 | 1 | 0 |
PABPC3 WILD-TYPE | 5 | 6 | 3 | 7 | 5 | 3 | 5 | 4 | 4 |
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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/KICH-TP/22569433/transformed.cor.cli.txt
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Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KICH-TP/22539844/KICH-TP.transferedmergedcluster.txt
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Number of patients = 66
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Number of significantly mutated genes = 8
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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.