This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 18 genes and 12 molecular subtypes across 220 patients, 38 significant findings detected with P value < 0.05 and Q value < 0.25.
-
ATRX mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
-
IDH1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
TP53 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
CIC mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
-
FUBP1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
NOTCH1 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
-
PIK3CA mutation correlated to 'METHLYATION_CNMF'.
-
PTEN mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Clinical Features |
MRNA CNMF |
MRNA CHIERARCHICAL |
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 | Chi-square test | Fisher's exact test | Chi-square test | Fisher's exact test | |
PTEN | 13 (6%) | 207 |
2.24e-07 (3.96e-05) |
6.77e-11 (1.25e-08) |
0.000979 (0.156) |
0.00248 (0.392) |
4.11e-07 (7.19e-05) |
0.000474 (0.0768) |
0.000594 (0.0957) |
0.000142 (0.0236) |
1.01e-08 (1.82e-06) |
1.18e-06 (0.000204) |
||
IDH1 | 167 (76%) | 53 |
0.225 (1.00) |
0.478 (1.00) |
1.38e-11 (2.57e-09) |
2.38e-32 (4.63e-30) |
4.02e-06 (0.000691) |
0.0871 (1.00) |
4.54e-09 (8.27e-07) |
0.027 (1.00) |
0.0194 (1.00) |
2.96e-05 (0.00503) |
5.92e-13 (1.11e-10) |
1.55e-15 (2.95e-13) |
CIC | 39 (18%) | 181 |
0.0502 (1.00) |
0.00351 (0.547) |
2.56e-08 (4.57e-06) |
7.83e-22 (1.51e-19) |
0.000206 (0.0339) |
0.528 (1.00) |
2.46e-05 (0.00421) |
4.54e-17 (8.68e-15) |
4.53e-05 (0.00756) |
0.362 (1.00) |
1.51e-07 (2.69e-05) |
0.0456 (1.00) |
TP53 | 116 (53%) | 104 |
0.113 (1.00) |
0.0133 (1.00) |
3.84e-17 (7.36e-15) |
2.06e-41 (4.03e-39) |
0.0543 (1.00) |
0.838 (1.00) |
0.159 (1.00) |
8.69e-14 (1.64e-11) |
0.0268 (1.00) |
0.00444 (0.684) |
1.43e-10 (2.64e-08) |
4.42e-05 (0.00742) |
ATRX | 97 (44%) | 123 |
0.0256 (1.00) |
0.0671 (1.00) |
2.79e-11 (5.19e-09) |
8.28e-29 (1.61e-26) |
0.16 (1.00) |
0.932 (1.00) |
0.373 (1.00) |
5.86e-09 (1.06e-06) |
0.0411 (1.00) |
0.0356 (1.00) |
1.04e-06 (0.000181) |
0.00378 (0.586) |
FUBP1 | 21 (10%) | 199 |
0.0231 (1.00) |
0.00587 (0.898) |
0.000249 (0.0406) |
1.41e-09 (2.59e-07) |
0.0696 (1.00) |
0.666 (1.00) |
0.0176 (1.00) |
3.86e-07 (6.79e-05) |
0.0893 (1.00) |
0.932 (1.00) |
0.0592 (1.00) |
0.505 (1.00) |
NOTCH1 | 19 (9%) | 201 |
0.615 (1.00) |
0.237 (1.00) |
0.0423 (1.00) |
3.74e-05 (0.00631) |
0.104 (1.00) |
0.893 (1.00) |
0.0559 (1.00) |
0.000698 (0.112) |
0.0835 (1.00) |
0.0803 (1.00) |
0.0397 (1.00) |
0.0987 (1.00) |
PIK3CA | 19 (9%) | 201 |
0.301 (1.00) |
0.00017 (0.028) |
0.769 (1.00) |
0.079 (1.00) |
1 (1.00) |
0.326 (1.00) |
0.214 (1.00) |
0.854 (1.00) |
0.0482 (1.00) |
0.285 (1.00) |
||
IL32 | 9 (4%) | 211 |
0.128 (1.00) |
0.135 (1.00) |
0.551 (1.00) |
0.619 (1.00) |
0.636 (1.00) |
0.805 (1.00) |
0.425 (1.00) |
0.856 (1.00) |
0.791 (1.00) |
0.434 (1.00) |
||
IDH2 | 8 (4%) | 212 |
0.0805 (1.00) |
0.115 (1.00) |
1 (1.00) |
1 (1.00) |
0.0791 (1.00) |
0.00342 (0.536) |
0.145 (1.00) |
0.485 (1.00) |
0.216 (1.00) |
0.501 (1.00) |
||
PIK3R1 | 13 (6%) | 207 |
0.615 (1.00) |
0.856 (1.00) |
0.187 (1.00) |
0.065 (1.00) |
0.495 (1.00) |
1 (1.00) |
0.722 (1.00) |
0.311 (1.00) |
0.927 (1.00) |
1 (1.00) |
0.373 (1.00) |
0.927 (1.00) |
CREBZF | 4 (2%) | 216 |
0.384 (1.00) |
0.0499 (1.00) |
0.197 (1.00) |
0.154 (1.00) |
0.036 (1.00) |
0.065 (1.00) |
0.385 (1.00) |
0.061 (1.00) |
0.514 (1.00) |
0.128 (1.00) |
||
PCDHAC2 | 14 (6%) | 206 |
1 (1.00) |
1 (1.00) |
0.0167 (1.00) |
0.0287 (1.00) |
0.661 (1.00) |
0.302 (1.00) |
0.835 (1.00) |
0.865 (1.00) |
0.188 (1.00) |
0.0866 (1.00) |
0.883 (1.00) |
0.0577 (1.00) |
NOX4 | 5 (2%) | 215 |
0.215 (1.00) |
0.922 (1.00) |
0.309 (1.00) |
0.715 (1.00) |
0.379 (1.00) |
0.355 (1.00) |
0.598 (1.00) |
0.165 (1.00) |
0.749 (1.00) |
0.587 (1.00) |
||
ZNF57 | 6 (3%) | 214 |
0.103 (1.00) |
0.242 (1.00) |
0.449 (1.00) |
0.104 (1.00) |
0.0212 (1.00) |
0.0673 (1.00) |
0.321 (1.00) |
0.0735 (1.00) |
0.491 (1.00) |
0.0377 (1.00) |
||
EIF1AX | 3 (1%) | 217 |
1 (1.00) |
0.439 (1.00) |
0.704 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.433 (1.00) |
0.397 (1.00) |
0.245 (1.00) |
0.765 (1.00) |
||
DCP1B | 4 (2%) | 216 |
0.196 (1.00) |
0.403 (1.00) |
0.0144 (1.00) |
0.154 (1.00) |
1 (1.00) |
1 (1.00) |
0.394 (1.00) |
0.474 (1.00) |
0.205 (1.00) |
0.661 (1.00) |
||
NAB2 | 4 (2%) | 216 |
0.919 (1.00) |
0.233 (1.00) |
0.598 (1.00) |
0.11 (1.00) |
0.689 (1.00) |
0.146 (1.00) |
0.612 (1.00) |
0.723 (1.00) |
0.475 (1.00) |
1 (1.00) |
P value = 2.79e-11 (Fisher's exact test), Q value = 5.2e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 43 | 45 | 45 | 85 |
ATRX MUTATED | 36 | 17 | 26 | 18 |
ATRX WILD-TYPE | 7 | 28 | 19 | 67 |
P value = 8.28e-29 (Fisher's exact test), Q value = 1.6e-26
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 97 | 34 | 57 | 27 |
ATRX MUTATED | 81 | 4 | 2 | 9 |
ATRX WILD-TYPE | 16 | 30 | 55 | 18 |
P value = 5.86e-09 (Fisher's exact test), Q value = 1.1e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 111 | 76 |
ATRX MUTATED | 1 | 65 | 31 |
ATRX WILD-TYPE | 32 | 46 | 45 |
P value = 1.04e-06 (Chi-square test), Q value = 0.00018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 38 | 34 | 17 | 61 | 27 | 31 | 4 | 7 |
ATRX MUTATED | 31 | 7 | 11 | 21 | 7 | 14 | 3 | 2 |
ATRX WILD-TYPE | 7 | 27 | 6 | 40 | 20 | 17 | 1 | 5 |
P value = 1.38e-11 (Fisher's exact test), Q value = 2.6e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 43 | 45 | 45 | 85 |
IDH1 MUTATED | 42 | 16 | 36 | 72 |
IDH1 WILD-TYPE | 1 | 29 | 9 | 13 |
P value = 2.38e-32 (Fisher's exact test), Q value = 4.6e-30
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 97 | 34 | 57 | 27 |
IDH1 MUTATED | 95 | 0 | 52 | 16 |
IDH1 WILD-TYPE | 2 | 34 | 5 | 11 |
P value = 4.02e-06 (Fisher's exact test), Q value = 0.00069
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 49 | 61 | 63 |
IDH1 MUTATED | 29 | 25 | 57 | 50 |
IDH1 WILD-TYPE | 8 | 24 | 4 | 13 |
P value = 4.54e-09 (Fisher's exact test), Q value = 8.3e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 67 | 79 |
IDH1 MUTATED | 39 | 64 | 64 |
IDH1 WILD-TYPE | 35 | 3 | 15 |
P value = 2.96e-05 (Fisher's exact test), Q value = 0.005
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 14 | 118 | 87 |
IDH1 MUTATED | 3 | 92 | 71 |
IDH1 WILD-TYPE | 11 | 26 | 16 |
P value = 5.92e-13 (Chi-square test), Q value = 1.1e-10
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 38 | 34 | 17 | 61 | 27 | 31 | 4 | 7 |
IDH1 MUTATED | 38 | 8 | 16 | 46 | 24 | 23 | 4 | 7 |
IDH1 WILD-TYPE | 0 | 26 | 1 | 15 | 3 | 8 | 0 | 0 |
P value = 1.55e-15 (Fisher's exact test), Q value = 3e-13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 87 | 97 |
IDH1 MUTATED | 6 | 76 | 84 |
IDH1 WILD-TYPE | 29 | 11 | 13 |
P value = 3.84e-17 (Fisher's exact test), Q value = 7.4e-15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 43 | 45 | 45 | 85 |
TP53 MUTATED | 42 | 19 | 33 | 22 |
TP53 WILD-TYPE | 1 | 26 | 12 | 63 |
P value = 2.06e-41 (Fisher's exact test), Q value = 4e-39
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 97 | 34 | 57 | 27 |
TP53 MUTATED | 95 | 7 | 2 | 11 |
TP53 WILD-TYPE | 2 | 27 | 55 | 16 |
P value = 8.69e-14 (Fisher's exact test), Q value = 1.6e-11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 111 | 76 |
TP53 MUTATED | 1 | 81 | 34 |
TP53 WILD-TYPE | 32 | 30 | 42 |
P value = 1.43e-10 (Chi-square test), Q value = 2.6e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 38 | 34 | 17 | 61 | 27 | 31 | 4 | 7 |
TP53 MUTATED | 37 | 9 | 14 | 26 | 7 | 15 | 4 | 3 |
TP53 WILD-TYPE | 1 | 25 | 3 | 35 | 20 | 16 | 0 | 4 |
P value = 4.42e-05 (Fisher's exact test), Q value = 0.0074
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 87 | 97 |
TP53 MUTATED | 11 | 61 | 43 |
TP53 WILD-TYPE | 24 | 26 | 54 |
P value = 2.56e-08 (Fisher's exact test), Q value = 4.6e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 43 | 45 | 45 | 85 |
CIC MUTATED | 0 | 1 | 9 | 29 |
CIC WILD-TYPE | 43 | 44 | 36 | 56 |
P value = 7.83e-22 (Fisher's exact test), Q value = 1.5e-19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 97 | 34 | 57 | 27 |
CIC MUTATED | 0 | 1 | 35 | 2 |
CIC WILD-TYPE | 97 | 33 | 22 | 25 |
P value = 0.000206 (Fisher's exact test), Q value = 0.034
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 49 | 61 | 63 |
CIC MUTATED | 1 | 4 | 20 | 14 |
CIC WILD-TYPE | 36 | 45 | 41 | 49 |
P value = 2.46e-05 (Fisher's exact test), Q value = 0.0042
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 67 | 79 |
CIC MUTATED | 2 | 18 | 19 |
CIC WILD-TYPE | 72 | 49 | 60 |
P value = 4.54e-17 (Fisher's exact test), Q value = 8.7e-15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 111 | 76 |
CIC MUTATED | 22 | 1 | 16 |
CIC WILD-TYPE | 11 | 110 | 60 |
P value = 4.53e-05 (Chi-square test), Q value = 0.0076
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 51 | 34 | 71 | 15 | 48 |
CIC MUTATED | 6 | 1 | 15 | 9 | 8 |
CIC WILD-TYPE | 45 | 33 | 56 | 6 | 40 |
P value = 1.51e-07 (Chi-square test), Q value = 2.7e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 38 | 34 | 17 | 61 | 27 | 31 | 4 | 7 |
CIC MUTATED | 0 | 2 | 2 | 12 | 16 | 6 | 0 | 1 |
CIC WILD-TYPE | 38 | 32 | 15 | 49 | 11 | 25 | 4 | 6 |
P value = 0.000249 (Fisher's exact test), Q value = 0.041
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 43 | 45 | 45 | 85 |
FUBP1 MUTATED | 0 | 1 | 3 | 17 |
FUBP1 WILD-TYPE | 43 | 44 | 42 | 68 |
P value = 1.41e-09 (Fisher's exact test), Q value = 2.6e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 97 | 34 | 57 | 27 |
FUBP1 MUTATED | 0 | 1 | 17 | 0 |
FUBP1 WILD-TYPE | 97 | 33 | 40 | 27 |
P value = 3.86e-07 (Fisher's exact test), Q value = 6.8e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 111 | 76 |
FUBP1 MUTATED | 12 | 2 | 7 |
FUBP1 WILD-TYPE | 21 | 109 | 69 |
P value = 3.74e-05 (Fisher's exact test), Q value = 0.0063
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 97 | 34 | 57 | 27 |
NOTCH1 MUTATED | 3 | 1 | 14 | 0 |
NOTCH1 WILD-TYPE | 94 | 33 | 43 | 27 |
P value = 0.000698 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 111 | 76 |
NOTCH1 MUTATED | 8 | 3 | 8 |
NOTCH1 WILD-TYPE | 25 | 108 | 68 |
P value = 0.00017 (Fisher's exact test), Q value = 0.028
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 97 | 34 | 57 | 27 |
PIK3CA MUTATED | 1 | 5 | 11 | 2 |
PIK3CA WILD-TYPE | 96 | 29 | 46 | 25 |
P value = 2.24e-07 (Fisher's exact test), Q value = 4e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 43 | 45 | 45 | 85 |
PTEN MUTATED | 0 | 11 | 2 | 0 |
PTEN WILD-TYPE | 43 | 34 | 43 | 85 |
P value = 6.77e-11 (Fisher's exact test), Q value = 1.3e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 97 | 34 | 57 | 27 |
PTEN MUTATED | 0 | 12 | 0 | 0 |
PTEN WILD-TYPE | 97 | 22 | 57 | 27 |
P value = 0.000979 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 49 | 61 | 63 |
PTEN MUTATED | 1 | 8 | 2 | 0 |
PTEN WILD-TYPE | 36 | 41 | 59 | 63 |
P value = 4.11e-07 (Fisher's exact test), Q value = 7.2e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 67 | 79 |
PTEN MUTATED | 13 | 0 | 0 |
PTEN WILD-TYPE | 61 | 67 | 79 |
P value = 0.000474 (Fisher's exact test), Q value = 0.077
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 111 | 76 |
PTEN MUTATED | 0 | 13 | 0 |
PTEN WILD-TYPE | 33 | 98 | 76 |
P value = 0.000594 (Chi-square test), Q value = 0.096
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 51 | 34 | 71 | 15 | 48 |
PTEN MUTATED | 9 | 3 | 1 | 0 | 0 |
PTEN WILD-TYPE | 42 | 31 | 70 | 15 | 48 |
P value = 0.000142 (Fisher's exact test), Q value = 0.024
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 14 | 118 | 87 |
PTEN MUTATED | 4 | 9 | 0 |
PTEN WILD-TYPE | 10 | 109 | 87 |
P value = 1.01e-08 (Chi-square test), Q value = 1.8e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 38 | 34 | 17 | 61 | 27 | 31 | 4 | 7 |
PTEN MUTATED | 0 | 11 | 0 | 1 | 0 | 1 | 0 | 0 |
PTEN WILD-TYPE | 38 | 23 | 17 | 60 | 27 | 30 | 4 | 7 |
P value = 1.18e-06 (Fisher's exact test), Q value = 2e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 87 | 97 |
PTEN MUTATED | 9 | 4 | 0 |
PTEN WILD-TYPE | 26 | 83 | 97 |
-
Mutation data file = LGG-TP.mutsig.cluster.txt
-
Molecular subtypes file = LGG-TP.transferedmergedcluster.txt
-
Number of patients = 220
-
Number of significantly mutated genes = 18
-
Number of Molecular subtypes = 12
-
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 multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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.