This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 38 genes and 10 molecular subtypes across 248 patients, 26 significant findings detected with P value < 0.05 and Q value < 0.25.
-
CTNNB1 mutation correlated to 'MRNA_CNMF', 'CN_CNMF', 'RPPA_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
PIK3R1 mutation correlated to 'METHLYATION_CNMF'.
-
PTEN mutation correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
KRAS mutation correlated to 'MRNA_CHIERARCHICAL'.
-
TP53 mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
CTCF mutation correlated to 'CN_CNMF'.
-
ARID1A mutation correlated to 'CN_CNMF'.
-
SIN3A mutation correlated to 'MIRSEQ_CHIERARCHICAL'.
Clinical Features |
MRNA CNMF |
MRNA CHIERARCHICAL |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nMutated (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Chi-square test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
TP53 | 69 (28%) | 179 |
3.88e-05 (0.0129) |
1.72e-07 (5.84e-05) |
1.05e-28 (3.71e-26) |
1.13e-12 (3.94e-10) |
2.01e-05 (0.00674) |
0.0014 (0.457) |
2.25e-16 (7.92e-14) |
6.8e-15 (2.39e-12) |
3.68e-09 (1.26e-06) |
8.17e-09 (2.79e-06) |
PTEN | 161 (65%) | 87 |
0.00428 (1.00) |
0.000357 (0.118) |
1.45e-20 (5.11e-18) |
1.43e-12 (4.96e-10) |
0.0257 (1.00) |
0.183 (1.00) |
1.07e-13 (3.76e-11) |
1.87e-12 (6.48e-10) |
1.21e-09 (4.15e-07) |
5.92e-13 (2.07e-10) |
CTNNB1 | 74 (30%) | 174 |
4.9e-07 (0.000166) |
0.00115 (0.378) |
2.57e-05 (0.00861) |
0.00327 (1.00) |
1.29e-10 (4.43e-08) |
0.112 (1.00) |
4.21e-11 (1.45e-08) |
0.0115 (1.00) |
0.0196 (1.00) |
9.13e-06 (0.00308) |
PIK3R1 | 83 (33%) | 165 |
0.0667 (1.00) |
0.0221 (1.00) |
0.00515 (1.00) |
3.22e-05 (0.0108) |
0.649 (1.00) |
0.877 (1.00) |
0.00627 (1.00) |
0.0144 (1.00) |
0.0147 (1.00) |
0.00249 (0.805) |
KRAS | 53 (21%) | 195 |
0.203 (1.00) |
0.000742 (0.244) |
0.0035 (1.00) |
0.119 (1.00) |
0.297 (1.00) |
0.855 (1.00) |
0.00123 (0.402) |
0.922 (1.00) |
0.0421 (1.00) |
0.209 (1.00) |
CTCF | 45 (18%) | 203 |
0.149 (1.00) |
0.421 (1.00) |
0.000169 (0.0559) |
0.0481 (1.00) |
0.0784 (1.00) |
0.848 (1.00) |
0.00834 (1.00) |
0.00233 (0.755) |
0.0116 (1.00) |
0.134 (1.00) |
ARID1A | 83 (33%) | 165 |
0.265 (1.00) |
0.0115 (1.00) |
5.37e-06 (0.00181) |
0.233 (1.00) |
0.0271 (1.00) |
1 (1.00) |
0.0478 (1.00) |
0.00899 (1.00) |
0.0204 (1.00) |
0.144 (1.00) |
SIN3A | 21 (8%) | 227 |
0.00479 (1.00) |
0.604 (1.00) |
0.00607 (1.00) |
0.129 (1.00) |
0.19 (1.00) |
0.000116 (0.0384) |
0.511 (1.00) |
0.457 (1.00) |
||
PPP2R1A | 27 (11%) | 221 |
0.076 (1.00) |
0.0518 (1.00) |
0.0284 (1.00) |
0.0121 (1.00) |
0.141 (1.00) |
0.313 (1.00) |
0.0531 (1.00) |
0.00974 (1.00) |
0.0665 (1.00) |
0.0052 (1.00) |
PIK3CA | 132 (53%) | 116 |
0.859 (1.00) |
0.203 (1.00) |
0.529 (1.00) |
0.678 (1.00) |
0.366 (1.00) |
0.365 (1.00) |
0.573 (1.00) |
0.523 (1.00) |
0.401 (1.00) |
0.502 (1.00) |
PRKAR1B | 4 (2%) | 244 |
0.99 (1.00) |
0.509 (1.00) |
0.887 (1.00) |
1 (1.00) |
0.506 (1.00) |
0.116 (1.00) |
0.789 (1.00) |
0.691 (1.00) |
||
RPL22 | 31 (12%) | 217 |
0.0531 (1.00) |
0.16 (1.00) |
0.0116 (1.00) |
0.00862 (1.00) |
0.0153 (1.00) |
0.26 (1.00) |
0.438 (1.00) |
0.0496 (1.00) |
0.213 (1.00) |
0.901 (1.00) |
FBXW7 | 39 (16%) | 209 |
0.225 (1.00) |
0.692 (1.00) |
0.339 (1.00) |
0.0677 (1.00) |
0.106 (1.00) |
0.107 (1.00) |
0.0442 (1.00) |
0.147 (1.00) |
0.356 (1.00) |
0.0798 (1.00) |
SPOP | 21 (8%) | 227 |
0.349 (1.00) |
1 (1.00) |
0.909 (1.00) |
0.356 (1.00) |
0.834 (1.00) |
0.415 (1.00) |
0.0337 (1.00) |
0.654 (1.00) |
0.606 (1.00) |
0.799 (1.00) |
ARID5B | 29 (12%) | 219 |
0.961 (1.00) |
0.459 (1.00) |
0.05 (1.00) |
0.136 (1.00) |
0.164 (1.00) |
0.182 (1.00) |
0.0622 (1.00) |
0.407 (1.00) |
0.342 (1.00) |
0.593 (1.00) |
FGFR2 | 31 (12%) | 217 |
0.385 (1.00) |
0.293 (1.00) |
0.364 (1.00) |
0.897 (1.00) |
0.97 (1.00) |
0.829 (1.00) |
0.911 (1.00) |
0.0492 (1.00) |
0.647 (1.00) |
1 (1.00) |
CCND1 | 15 (6%) | 233 |
0.631 (1.00) |
0.833 (1.00) |
0.124 (1.00) |
0.495 (1.00) |
0.374 (1.00) |
0.338 (1.00) |
0.0595 (1.00) |
0.21 (1.00) |
0.43 (1.00) |
0.757 (1.00) |
SMTNL2 | 9 (4%) | 239 |
0.188 (1.00) |
0.588 (1.00) |
0.603 (1.00) |
1 (1.00) |
0.831 (1.00) |
0.0235 (1.00) |
0.789 (1.00) |
1 (1.00) |
||
NFE2L2 | 15 (6%) | 233 |
0.0905 (1.00) |
0.833 (1.00) |
0.00201 (0.652) |
0.631 (1.00) |
0.248 (1.00) |
1 (1.00) |
0.538 (1.00) |
0.62 (1.00) |
0.342 (1.00) |
0.593 (1.00) |
CHD4 | 35 (14%) | 213 |
0.0986 (1.00) |
0.284 (1.00) |
0.551 (1.00) |
0.907 (1.00) |
0.97 (1.00) |
0.287 (1.00) |
0.563 (1.00) |
0.698 (1.00) |
0.471 (1.00) |
0.951 (1.00) |
RBMX | 13 (5%) | 235 |
0.191 (1.00) |
0.18 (1.00) |
0.233 (1.00) |
0.386 (1.00) |
0.0124 (1.00) |
1 (1.00) |
0.0912 (1.00) |
0.106 (1.00) |
0.813 (1.00) |
0.868 (1.00) |
FAM9A | 14 (6%) | 234 |
0.84 (1.00) |
0.27 (1.00) |
0.178 (1.00) |
0.0227 (1.00) |
0.384 (1.00) |
0.0329 (1.00) |
0.0266 (1.00) |
0.225 (1.00) |
||
MORC4 | 20 (8%) | 228 |
0.583 (1.00) |
0.18 (1.00) |
0.0651 (1.00) |
0.28 (1.00) |
0.212 (1.00) |
0.0332 (1.00) |
0.341 (1.00) |
0.119 (1.00) |
0.317 (1.00) |
0.562 (1.00) |
HPD | 7 (3%) | 241 |
0.564 (1.00) |
0.776 (1.00) |
0.447 (1.00) |
0.651 (1.00) |
0.0411 (1.00) |
0.592 (1.00) |
1 (1.00) |
1 (1.00) |
||
CASP8 | 17 (7%) | 231 |
0.381 (1.00) |
0.0595 (1.00) |
0.119 (1.00) |
0.626 (1.00) |
0.154 (1.00) |
0.269 (1.00) |
0.134 (1.00) |
0.031 (1.00) |
0.464 (1.00) |
1 (1.00) |
FOXA2 | 12 (5%) | 236 |
0.507 (1.00) |
0.795 (1.00) |
0.0719 (1.00) |
0.744 (1.00) |
0.0551 (1.00) |
1 (1.00) |
0.678 (1.00) |
0.778 (1.00) |
||
ABI1 | 4 (2%) | 244 |
0.821 (1.00) |
0.64 (1.00) |
0.637 (1.00) |
0.67 (1.00) |
0.702 (1.00) |
|||||
DNER | 18 (7%) | 230 |
0.191 (1.00) |
0.0515 (1.00) |
0.00333 (1.00) |
0.597 (1.00) |
0.0217 (1.00) |
0.581 (1.00) |
0.751 (1.00) |
0.0168 (1.00) |
1 (1.00) |
0.881 (1.00) |
BCOR | 30 (12%) | 218 |
0.687 (1.00) |
0.405 (1.00) |
0.00798 (1.00) |
0.0253 (1.00) |
0.512 (1.00) |
0.5 (1.00) |
0.027 (1.00) |
0.0458 (1.00) |
0.863 (1.00) |
0.44 (1.00) |
BRS3 | 15 (6%) | 233 |
0.536 (1.00) |
0.151 (1.00) |
0.15 (1.00) |
0.519 (1.00) |
0.392 (1.00) |
0.54 (1.00) |
0.143 (1.00) |
0.0329 (1.00) |
0.551 (1.00) |
0.589 (1.00) |
NRAS | 9 (4%) | 239 |
0.645 (1.00) |
0.316 (1.00) |
1 (1.00) |
0.589 (1.00) |
0.357 (1.00) |
|||||
SGK1 | 15 (6%) | 233 |
0.381 (1.00) |
0.0595 (1.00) |
0.0598 (1.00) |
0.625 (1.00) |
0.226 (1.00) |
0.0954 (1.00) |
0.288 (1.00) |
0.601 (1.00) |
0.813 (1.00) |
0.868 (1.00) |
TIAL1 | 11 (4%) | 237 |
0.381 (1.00) |
0.405 (1.00) |
0.303 (1.00) |
0.0634 (1.00) |
0.564 (1.00) |
0.744 (1.00) |
0.551 (1.00) |
0.508 (1.00) |
0.342 (1.00) |
0.725 (1.00) |
RPL14 | 7 (3%) | 241 |
0.902 (1.00) |
0.874 (1.00) |
0.479 (1.00) |
1 (1.00) |
0.343 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
SLC48A1 | 5 (2%) | 243 |
0.736 (1.00) |
0.639 (1.00) |
0.803 (1.00) |
0.372 (1.00) |
0.886 (1.00) |
0.517 (1.00) |
0.789 (1.00) |
0.691 (1.00) |
||
ZFHX3 | 44 (18%) | 204 |
0.375 (1.00) |
0.0299 (1.00) |
0.0451 (1.00) |
0.0629 (1.00) |
0.318 (1.00) |
0.179 (1.00) |
0.139 (1.00) |
0.789 (1.00) |
0.536 (1.00) |
0.974 (1.00) |
RNF43 | 12 (5%) | 236 |
0.133 (1.00) |
0.151 (1.00) |
0.215 (1.00) |
0.377 (1.00) |
0.296 (1.00) |
1 (1.00) |
0.128 (1.00) |
0.0688 (1.00) |
0.338 (1.00) |
0.262 (1.00) |
ZNF263 | 8 (3%) | 240 |
0.0242 (1.00) |
0.0595 (1.00) |
0.483 (1.00) |
0.386 (1.00) |
0.611 (1.00) |
1 (1.00) |
0.464 (1.00) |
1 (1.00) |
0.43 (1.00) |
0.589 (1.00) |
P value = 4.9e-07 (Fisher's exact test), Q value = 0.00017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 12 | 18 | 11 | 10 |
CTNNB1 MUTATED | 0 | 3 | 4 | 10 |
CTNNB1 WILD-TYPE | 12 | 15 | 7 | 0 |
P value = 2.57e-05 (Chi-square test), Q value = 0.0086
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 157 | 5 | 56 | 6 | 10 | 8 |
CTNNB1 MUTATED | 59 | 2 | 2 | 4 | 4 | 1 |
CTNNB1 WILD-TYPE | 98 | 3 | 54 | 2 | 6 | 7 |
P value = 1.29e-10 (Chi-square test), Q value = 4.4e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 39 | 36 | 37 | 10 | 40 | 24 |
CTNNB1 MUTATED | 6 | 10 | 6 | 0 | 32 | 10 |
CTNNB1 WILD-TYPE | 33 | 26 | 31 | 10 | 8 | 14 |
P value = 4.21e-11 (Chi-square test), Q value = 1.5e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 45 | 74 | 24 | 27 | 70 |
CTNNB1 MUTATED | 1 | 13 | 6 | 20 | 31 |
CTNNB1 WILD-TYPE | 44 | 61 | 18 | 7 | 39 |
P value = 9.13e-06 (Fisher's exact test), Q value = 0.0031
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 22 | 57 | 27 | 10 |
CTNNB1 MUTATED | 2 | 16 | 1 | 8 |
CTNNB1 WILD-TYPE | 20 | 41 | 26 | 2 |
P value = 3.22e-05 (Fisher's exact test), Q value = 0.011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 43 | 41 | 51 |
PIK3R1 MUTATED | 5 | 12 | 28 |
PIK3R1 WILD-TYPE | 38 | 29 | 23 |
P value = 0.000357 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 17 | 18 | 16 |
PTEN MUTATED | 15 | 14 | 4 |
PTEN WILD-TYPE | 2 | 4 | 12 |
P value = 1.45e-20 (Chi-square test), Q value = 5.1e-18
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 157 | 5 | 56 | 6 | 10 | 8 |
PTEN MUTATED | 130 | 2 | 5 | 5 | 7 | 7 |
PTEN WILD-TYPE | 27 | 3 | 51 | 1 | 3 | 1 |
P value = 1.43e-12 (Fisher's exact test), Q value = 5e-10
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 43 | 41 | 51 |
PTEN MUTATED | 7 | 30 | 44 |
PTEN WILD-TYPE | 36 | 11 | 7 |
P value = 1.07e-13 (Chi-square test), Q value = 3.8e-11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 45 | 74 | 24 | 27 | 70 |
PTEN MUTATED | 9 | 68 | 13 | 18 | 50 |
PTEN WILD-TYPE | 36 | 6 | 11 | 9 | 20 |
P value = 1.87e-12 (Fisher's exact test), Q value = 6.5e-10
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 10 | 136 | 94 |
PTEN MUTATED | 9 | 113 | 36 |
PTEN WILD-TYPE | 1 | 23 | 58 |
P value = 1.21e-09 (Fisher's exact test), Q value = 4.1e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 36 | 55 | 25 |
PTEN MUTATED | 10 | 49 | 11 |
PTEN WILD-TYPE | 26 | 6 | 14 |
P value = 5.92e-13 (Fisher's exact test), Q value = 2.1e-10
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 22 | 57 | 27 | 10 |
PTEN MUTATED | 6 | 52 | 5 | 7 |
PTEN WILD-TYPE | 16 | 5 | 22 | 3 |
P value = 0.000742 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 17 | 18 | 16 |
KRAS MUTATED | 9 | 1 | 1 |
KRAS WILD-TYPE | 8 | 17 | 15 |
P value = 3.88e-05 (Fisher's exact test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 12 | 18 | 11 | 10 |
TP53 MUTATED | 2 | 13 | 1 | 0 |
TP53 WILD-TYPE | 10 | 5 | 10 | 10 |
P value = 1.72e-07 (Fisher's exact test), Q value = 5.8e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 17 | 18 | 16 |
TP53 MUTATED | 3 | 0 | 13 |
TP53 WILD-TYPE | 14 | 18 | 3 |
P value = 1.05e-28 (Chi-square test), Q value = 3.7e-26
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 157 | 5 | 56 | 6 | 10 | 8 |
TP53 MUTATED | 11 | 2 | 50 | 0 | 3 | 2 |
TP53 WILD-TYPE | 146 | 3 | 6 | 6 | 7 | 6 |
P value = 1.13e-12 (Fisher's exact test), Q value = 3.9e-10
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 43 | 41 | 51 |
TP53 MUTATED | 31 | 4 | 5 |
TP53 WILD-TYPE | 12 | 37 | 46 |
P value = 2.01e-05 (Chi-square test), Q value = 0.0067
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 39 | 36 | 37 | 10 | 40 | 24 |
TP53 MUTATED | 9 | 19 | 4 | 2 | 2 | 8 |
TP53 WILD-TYPE | 30 | 17 | 33 | 8 | 38 | 16 |
P value = 2.25e-16 (Chi-square test), Q value = 7.9e-14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 45 | 74 | 24 | 27 | 70 |
TP53 MUTATED | 35 | 5 | 7 | 4 | 13 |
TP53 WILD-TYPE | 10 | 69 | 17 | 23 | 57 |
P value = 6.8e-15 (Fisher's exact test), Q value = 2.4e-12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 10 | 136 | 94 |
TP53 MUTATED | 6 | 10 | 48 |
TP53 WILD-TYPE | 4 | 126 | 46 |
P value = 3.68e-09 (Fisher's exact test), Q value = 1.3e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 36 | 55 | 25 |
TP53 MUTATED | 25 | 5 | 6 |
TP53 WILD-TYPE | 11 | 50 | 19 |
P value = 8.17e-09 (Fisher's exact test), Q value = 2.8e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 22 | 57 | 27 | 10 |
TP53 MUTATED | 9 | 5 | 20 | 2 |
TP53 WILD-TYPE | 13 | 52 | 7 | 8 |
P value = 0.000169 (Chi-square test), Q value = 0.056
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 157 | 5 | 56 | 6 | 10 | 8 |
CTCF MUTATED | 39 | 0 | 0 | 0 | 0 | 3 |
CTCF WILD-TYPE | 118 | 5 | 56 | 6 | 10 | 5 |
P value = 5.37e-06 (Chi-square test), Q value = 0.0018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 157 | 5 | 56 | 6 | 10 | 8 |
ARID1A MUTATED | 69 | 2 | 4 | 1 | 0 | 4 |
ARID1A WILD-TYPE | 88 | 3 | 52 | 5 | 10 | 4 |
P value = 0.000116 (Fisher's exact test), Q value = 0.038
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 10 | 136 | 94 |
SIN3A MUTATED | 4 | 4 | 13 |
SIN3A WILD-TYPE | 6 | 132 | 81 |
-
Mutation data file = UCEC-TP.mutsig.cluster.txt
-
Molecular subtypes file = UCEC-TP.transferedmergedcluster.txt
-
Number of patients = 248
-
Number of significantly mutated genes = 38
-
Number of Molecular subtypes = 10
-
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.