This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 37 genes and 10 molecular subtypes across 217 patients, 38 significant findings detected with P value < 0.05 and Q value < 0.25.
-
IDH1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
-
TP53 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
PIK3CA mutation correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
ATRX mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
FUBP1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
CIC mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
-
NOTCH1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
PTEN mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
-
NF1 mutation correlated to 'METHLYATION_CNMF'.
-
EGFR mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Clinical Features |
MRNA CNMF |
MRNA CHIERARCHICAL |
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 | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | |
TP53 | 113 (52%) | 104 |
0.113 (1.00) |
0.0133 (1.00) |
2.78e-23 (8.52e-21) |
1.52e-42 (4.71e-40) |
9.59e-16 (2.9e-13) |
5.01e-12 (1.49e-09) |
0.000891 (0.243) |
0.0181 (1.00) |
0.0347 (1.00) |
0.000326 (0.0904) |
CIC | 41 (19%) | 176 |
0.0502 (1.00) |
0.00351 (0.919) |
6.22e-19 (1.89e-16) |
1.87e-22 (5.72e-20) |
4.98e-13 (1.49e-10) |
5.58e-15 (1.67e-12) |
1.43e-06 (0.00041) |
0.00468 (1.00) |
0.00262 (0.693) |
0.00255 (0.678) |
NOTCH1 | 19 (9%) | 198 |
0.615 (1.00) |
0.237 (1.00) |
1.01e-05 (0.00287) |
2.29e-06 (0.000654) |
0.000143 (0.0403) |
2.65e-05 (0.00748) |
0.00323 (0.848) |
0.000941 (0.256) |
0.0674 (1.00) |
0.000148 (0.0414) |
PTEN | 12 (6%) | 205 |
6.19e-09 (1.81e-06) |
2.01e-10 (5.93e-08) |
2.43e-11 (7.19e-09) |
0.00194 (0.52) |
0.000294 (0.0816) |
0.0174 (1.00) |
0.000234 (0.0653) |
0.00428 (1.00) |
||
ATRX | 93 (43%) | 124 |
0.0256 (1.00) |
0.0671 (1.00) |
3.04e-15 (9.15e-13) |
5.99e-29 (1.85e-26) |
1.17e-16 (3.53e-14) |
1.15e-08 (3.35e-06) |
0.00191 (0.514) |
0.0485 (1.00) |
0.0352 (1.00) |
0.00673 (1.00) |
FUBP1 | 22 (10%) | 195 |
0.0231 (1.00) |
0.00587 (1.00) |
1.06e-09 (3.11e-07) |
3.41e-08 (9.9e-06) |
1.98e-08 (5.75e-06) |
2e-07 (5.79e-05) |
0.0194 (1.00) |
0.222 (1.00) |
0.146 (1.00) |
0.222 (1.00) |
IDH1 | 165 (76%) | 52 |
0.225 (1.00) |
0.478 (1.00) |
1.02e-12 (3.04e-10) |
4.6e-32 (1.42e-29) |
1.8e-19 (5.48e-17) |
0.0595 (1.00) |
0.0684 (1.00) |
0.106 (1.00) |
0.00254 (0.678) |
0.00361 (0.943) |
EGFR | 10 (5%) | 207 |
7.43e-06 (0.00211) |
2.92e-07 (8.42e-05) |
0.000501 (0.138) |
0.45 (1.00) |
0.162 (1.00) |
0.835 (1.00) |
0.567 (1.00) |
0.826 (1.00) |
||
PIK3CA | 19 (9%) | 198 |
0.000509 (0.14) |
0.000333 (0.092) |
0.0642 (1.00) |
0.345 (1.00) |
0.4 (1.00) |
0.246 (1.00) |
0.496 (1.00) |
0.585 (1.00) |
||
NF1 | 16 (7%) | 201 |
0.0451 (1.00) |
2.4e-06 (0.000684) |
0.00101 (0.273) |
0.774 (1.00) |
0.426 (1.00) |
0.551 (1.00) |
0.128 (1.00) |
0.187 (1.00) |
||
IDH2 | 9 (4%) | 208 |
0.103 (1.00) |
0.0849 (1.00) |
0.0501 (1.00) |
0.00158 (0.426) |
0.0207 (1.00) |
0.509 (1.00) |
0.488 (1.00) |
0.488 (1.00) |
||
IL32 | 6 (3%) | 211 |
0.0609 (1.00) |
0.0376 (1.00) |
0.33 (1.00) |
0.304 (1.00) |
0.357 (1.00) |
0.28 (1.00) |
0.527 (1.00) |
0.522 (1.00) |
||
PIK3R1 | 14 (6%) | 203 |
0.615 (1.00) |
0.856 (1.00) |
0.00526 (1.00) |
0.0488 (1.00) |
0.5 (1.00) |
0.451 (1.00) |
0.875 (1.00) |
1 (1.00) |
0.0717 (1.00) |
1 (1.00) |
ZNF844 | 6 (3%) | 211 |
1 (1.00) |
0.6 (1.00) |
0.442 (1.00) |
0.628 (1.00) |
0.185 (1.00) |
1 (1.00) |
0.188 (1.00) |
0.746 (1.00) |
||
TCF12 | 9 (4%) | 208 |
0.907 (1.00) |
0.725 (1.00) |
0.571 (1.00) |
0.193 (1.00) |
0.39 (1.00) |
0.812 (1.00) |
0.328 (1.00) |
0.488 (1.00) |
||
ZBTB20 | 10 (5%) | 207 |
0.415 (1.00) |
0.368 (1.00) |
0.562 (1.00) |
0.908 (1.00) |
0.911 (1.00) |
0.45 (1.00) |
0.417 (1.00) |
1 (1.00) |
||
TIMD4 | 6 (3%) | 211 |
0.577 (1.00) |
1 (1.00) |
0.711 (1.00) |
0.858 (1.00) |
0.554 (1.00) |
0.754 (1.00) |
0.283 (1.00) |
0.26 (1.00) |
||
CREBZF | 4 (2%) | 213 |
0.161 (1.00) |
0.06 (1.00) |
0.356 (1.00) |
0.0581 (1.00) |
0.343 (1.00) |
0.0769 (1.00) |
0.139 (1.00) |
0.0728 (1.00) |
||
ZNF57 | 6 (3%) | 211 |
0.131 (1.00) |
0.183 (1.00) |
0.0976 (1.00) |
0.085 (1.00) |
0.0274 (1.00) |
0.382 (1.00) |
0.478 (1.00) |
0.363 (1.00) |
||
ARID1A | 13 (6%) | 204 |
0.866 (1.00) |
0.508 (1.00) |
0.381 (1.00) |
0.277 (1.00) |
0.339 (1.00) |
0.745 (1.00) |
0.356 (1.00) |
0.729 (1.00) |
||
EMG1 | 4 (2%) | 213 |
0.683 (1.00) |
0.802 (1.00) |
0.97 (1.00) |
0.642 (1.00) |
0.226 (1.00) |
0.68 (1.00) |
0.0685 (1.00) |
0.673 (1.00) |
||
PRAMEF11 | 6 (3%) | 211 |
1 (1.00) |
0.413 (1.00) |
0.213 (1.00) |
0.242 (1.00) |
0.222 (1.00) |
0.0269 (1.00) |
0.503 (1.00) |
0.023 (1.00) |
||
PRDM9 | 6 (3%) | 211 |
0.659 (1.00) |
0.183 (1.00) |
0.305 (1.00) |
0.858 (1.00) |
0.437 (1.00) |
1 (1.00) |
0.65 (1.00) |
1 (1.00) |
||
NOX4 | 5 (2%) | 212 |
0.102 (1.00) |
0.858 (1.00) |
0.594 (1.00) |
0.238 (1.00) |
0.865 (1.00) |
0.323 (1.00) |
0.696 (1.00) |
0.307 (1.00) |
||
ANKRD30A | 8 (4%) | 209 |
0.529 (1.00) |
0.207 (1.00) |
0.841 (1.00) |
1 (1.00) |
0.503 (1.00) |
0.302 (1.00) |
0.836 (1.00) |
0.228 (1.00) |
||
MUC7 | 5 (2%) | 212 |
0.24 (1.00) |
0.22 (1.00) |
0.401 (1.00) |
0.57 (1.00) |
0.805 (1.00) |
0.72 (1.00) |
0.412 (1.00) |
1 (1.00) |
||
PAX4 | 5 (2%) | 212 |
0.453 (1.00) |
0.858 (1.00) |
0.757 (1.00) |
0.705 (1.00) |
0.473 (1.00) |
0.72 (1.00) |
0.448 (1.00) |
0.715 (1.00) |
||
ZNF845 | 6 (3%) | 211 |
0.278 (1.00) |
0.773 (1.00) |
0.711 (1.00) |
0.628 (1.00) |
0.839 (1.00) |
0.535 (1.00) |
0.934 (1.00) |
0.522 (1.00) |
||
C15ORF2 | 8 (4%) | 209 |
0.239 (1.00) |
0.287 (1.00) |
0.0132 (1.00) |
0.318 (1.00) |
0.69 (1.00) |
0.302 (1.00) |
0.601 (1.00) |
0.0956 (1.00) |
||
SPDYE5 | 4 (2%) | 213 |
0.0526 (1.00) |
0.0258 (1.00) |
0.0565 (1.00) |
0.286 (1.00) |
0.0712 (1.00) |
0.25 (1.00) |
0.266 (1.00) |
0.0352 (1.00) |
||
SCAF1 | 4 (2%) | 213 |
1 (1.00) |
1 (1.00) |
0.424 (1.00) |
0.373 (1.00) |
0.0853 (1.00) |
1 (1.00) |
0.807 (1.00) |
1 (1.00) |
||
FSTL5 | 6 (3%) | 211 |
0.0609 (1.00) |
0.242 (1.00) |
0.118 (1.00) |
0.0256 (1.00) |
0.0875 (1.00) |
0.382 (1.00) |
0.42 (1.00) |
0.363 (1.00) |
||
C9ORF79 | 8 (4%) | 209 |
1 (1.00) |
0.555 (1.00) |
0.657 (1.00) |
0.779 (1.00) |
0.792 (1.00) |
0.801 (1.00) |
0.756 (1.00) |
0.792 (1.00) |
||
ZCCHC12 | 3 (1%) | 214 |
0.0543 (1.00) |
0.0531 (1.00) |
0.546 (1.00) |
0.144 (1.00) |
0.434 (1.00) |
0.191 (1.00) |
0.656 (1.00) |
0.181 (1.00) |
||
SMARCA4 | 13 (6%) | 204 |
0.714 (1.00) |
0.465 (1.00) |
0.5 (1.00) |
0.676 (1.00) |
0.35 (1.00) |
0.412 (1.00) |
0.0555 (1.00) |
0.188 (1.00) |
||
MYH4 | 5 (2%) | 212 |
0.453 (1.00) |
0.858 (1.00) |
0.418 (1.00) |
0.107 (1.00) |
0.00846 (1.00) |
0.72 (1.00) |
0.00307 (0.811) |
0.715 (1.00) |
||
TRDN | 4 (2%) | 213 |
0.448 (1.00) |
1 (1.00) |
0.97 (1.00) |
0.642 (1.00) |
1 (1.00) |
0.427 (1.00) |
0.434 (1.00) |
0.418 (1.00) |
P value = 1.02e-12 (Fisher's exact test), Q value = 3e-10
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 49 | 76 |
IDH1 MUTATED | 78 | 17 | 69 |
IDH1 WILD-TYPE | 12 | 32 | 7 |
P value = 4.6e-32 (Fisher's exact test), Q value = 1.4e-29
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 32 | 28 | 56 |
IDH1 MUTATED | 94 | 0 | 15 | 52 |
IDH1 WILD-TYPE | 2 | 32 | 13 | 4 |
P value = 1.8e-19 (Chi-square test), Q value = 5.5e-17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 58 | 40 | 36 | 71 | 10 |
IDH1 MUTATED | 58 | 8 | 33 | 56 | 9 |
IDH1 WILD-TYPE | 0 | 32 | 3 | 15 | 1 |
P value = 2.78e-23 (Fisher's exact test), Q value = 8.5e-21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 49 | 76 |
TP53 MUTATED | 80 | 22 | 11 |
TP53 WILD-TYPE | 10 | 27 | 65 |
P value = 1.52e-42 (Fisher's exact test), Q value = 4.7e-40
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 32 | 28 | 56 |
TP53 MUTATED | 95 | 6 | 8 | 3 |
TP53 WILD-TYPE | 1 | 26 | 20 | 53 |
P value = 9.59e-16 (Chi-square test), Q value = 2.9e-13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 58 | 40 | 36 | 71 | 10 |
TP53 MUTATED | 56 | 14 | 4 | 32 | 6 |
TP53 WILD-TYPE | 2 | 26 | 32 | 39 | 4 |
P value = 5.01e-12 (Fisher's exact test), Q value = 1.5e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 112 | 70 |
TP53 MUTATED | 2 | 80 | 30 |
TP53 WILD-TYPE | 31 | 32 | 40 |
P value = 0.000891 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 55 | 33 | 82 | 46 |
TP53 MUTATED | 35 | 12 | 33 | 32 |
TP53 WILD-TYPE | 20 | 21 | 49 | 14 |
P value = 0.000326 (Fisher's exact test), Q value = 0.09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 7 | 113 | 96 |
TP53 MUTATED | 1 | 72 | 39 |
TP53 WILD-TYPE | 6 | 41 | 57 |
P value = 0.000509 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 49 | 76 |
PIK3CA MUTATED | 1 | 5 | 13 |
PIK3CA WILD-TYPE | 89 | 44 | 63 |
P value = 0.000333 (Fisher's exact test), Q value = 0.092
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 32 | 28 | 56 |
PIK3CA MUTATED | 1 | 5 | 3 | 10 |
PIK3CA WILD-TYPE | 95 | 27 | 25 | 46 |
P value = 3.04e-15 (Fisher's exact test), Q value = 9.2e-13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 49 | 76 |
ATRX MUTATED | 66 | 17 | 10 |
ATRX WILD-TYPE | 24 | 32 | 66 |
P value = 5.99e-29 (Fisher's exact test), Q value = 1.8e-26
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 32 | 28 | 56 |
ATRX MUTATED | 80 | 4 | 6 | 2 |
ATRX WILD-TYPE | 16 | 28 | 22 | 54 |
P value = 1.17e-16 (Chi-square test), Q value = 3.5e-14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 58 | 40 | 36 | 71 | 10 |
ATRX MUTATED | 52 | 10 | 2 | 26 | 2 |
ATRX WILD-TYPE | 6 | 30 | 34 | 45 | 8 |
P value = 1.15e-08 (Fisher's exact test), Q value = 3.4e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 112 | 70 |
ATRX MUTATED | 1 | 64 | 27 |
ATRX WILD-TYPE | 32 | 48 | 43 |
P value = 1.06e-09 (Fisher's exact test), Q value = 3.1e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 49 | 76 |
FUBP1 MUTATED | 0 | 1 | 21 |
FUBP1 WILD-TYPE | 90 | 48 | 55 |
P value = 3.41e-08 (Fisher's exact test), Q value = 9.9e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 32 | 28 | 56 |
FUBP1 MUTATED | 0 | 1 | 2 | 16 |
FUBP1 WILD-TYPE | 96 | 31 | 26 | 40 |
P value = 1.98e-08 (Chi-square test), Q value = 5.7e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 58 | 40 | 36 | 71 | 10 |
FUBP1 MUTATED | 0 | 1 | 14 | 6 | 1 |
FUBP1 WILD-TYPE | 58 | 39 | 22 | 65 | 9 |
P value = 2e-07 (Fisher's exact test), Q value = 5.8e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 112 | 70 |
FUBP1 MUTATED | 13 | 3 | 6 |
FUBP1 WILD-TYPE | 20 | 109 | 64 |
P value = 6.22e-19 (Fisher's exact test), Q value = 1.9e-16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 49 | 76 |
CIC MUTATED | 1 | 1 | 39 |
CIC WILD-TYPE | 89 | 48 | 37 |
P value = 1.87e-22 (Fisher's exact test), Q value = 5.7e-20
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 32 | 28 | 56 |
CIC MUTATED | 0 | 1 | 3 | 36 |
CIC WILD-TYPE | 96 | 31 | 25 | 20 |
P value = 4.98e-13 (Chi-square test), Q value = 1.5e-10
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 58 | 40 | 36 | 71 | 10 |
CIC MUTATED | 0 | 1 | 22 | 17 | 1 |
CIC WILD-TYPE | 58 | 39 | 14 | 54 | 9 |
P value = 5.58e-15 (Fisher's exact test), Q value = 1.7e-12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 112 | 70 |
CIC MUTATED | 22 | 3 | 16 |
CIC WILD-TYPE | 11 | 109 | 54 |
P value = 1.43e-06 (Fisher's exact test), Q value = 0.00041
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 55 | 33 | 82 | 46 |
CIC MUTATED | 6 | 16 | 18 | 1 |
CIC WILD-TYPE | 49 | 17 | 64 | 45 |
P value = 1.01e-05 (Fisher's exact test), Q value = 0.0029
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 49 | 76 |
NOTCH1 MUTATED | 1 | 2 | 16 |
NOTCH1 WILD-TYPE | 89 | 47 | 60 |
P value = 2.29e-06 (Fisher's exact test), Q value = 0.00065
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 32 | 28 | 56 |
NOTCH1 MUTATED | 2 | 1 | 0 | 15 |
NOTCH1 WILD-TYPE | 94 | 31 | 28 | 41 |
P value = 0.000143 (Chi-square test), Q value = 0.04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 58 | 40 | 36 | 71 | 10 |
NOTCH1 MUTATED | 1 | 1 | 10 | 7 | 0 |
NOTCH1 WILD-TYPE | 57 | 39 | 26 | 64 | 10 |
P value = 2.65e-05 (Fisher's exact test), Q value = 0.0075
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 112 | 70 |
NOTCH1 MUTATED | 9 | 2 | 8 |
NOTCH1 WILD-TYPE | 24 | 110 | 62 |
P value = 0.000148 (Fisher's exact test), Q value = 0.041
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 7 | 113 | 96 |
NOTCH1 MUTATED | 0 | 2 | 17 |
NOTCH1 WILD-TYPE | 7 | 111 | 79 |
P value = 6.19e-09 (Fisher's exact test), Q value = 1.8e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 49 | 76 |
PTEN MUTATED | 0 | 12 | 0 |
PTEN WILD-TYPE | 90 | 37 | 76 |
P value = 2.01e-10 (Fisher's exact test), Q value = 5.9e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 32 | 28 | 56 |
PTEN MUTATED | 0 | 11 | 0 | 0 |
PTEN WILD-TYPE | 96 | 21 | 28 | 56 |
P value = 2.43e-11 (Chi-square test), Q value = 7.2e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 58 | 40 | 36 | 71 | 10 |
PTEN MUTATED | 0 | 12 | 0 | 0 | 0 |
PTEN WILD-TYPE | 58 | 28 | 36 | 71 | 10 |
P value = 0.000294 (Fisher's exact test), Q value = 0.082
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 55 | 33 | 82 | 46 |
PTEN MUTATED | 8 | 0 | 0 | 4 |
PTEN WILD-TYPE | 47 | 33 | 82 | 42 |
P value = 0.000234 (Chi-square test), Q value = 0.065
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 37 | 28 | 71 | 33 | 28 | 19 |
PTEN MUTATED | 8 | 0 | 1 | 1 | 2 | 0 |
PTEN WILD-TYPE | 29 | 28 | 70 | 32 | 26 | 19 |
P value = 2.4e-06 (Fisher's exact test), Q value = 0.00068
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 32 | 28 | 56 |
NF1 MUTATED | 1 | 8 | 3 | 0 |
NF1 WILD-TYPE | 95 | 24 | 25 | 56 |
P value = 7.43e-06 (Fisher's exact test), Q value = 0.0021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 49 | 76 |
EGFR MUTATED | 1 | 9 | 0 |
EGFR WILD-TYPE | 89 | 40 | 76 |
P value = 2.92e-07 (Fisher's exact test), Q value = 8.4e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 32 | 28 | 56 |
EGFR MUTATED | 0 | 8 | 2 | 0 |
EGFR WILD-TYPE | 96 | 24 | 26 | 56 |
P value = 0.000501 (Chi-square test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 58 | 40 | 36 | 71 | 10 |
EGFR MUTATED | 0 | 7 | 0 | 3 | 0 |
EGFR WILD-TYPE | 58 | 33 | 36 | 68 | 10 |
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Mutation data file = LGG-TP.mutsig.cluster.txt
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Molecular subtypes file = LGG-TP.transferedmergedcluster.txt
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Number of patients = 217
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Number of significantly mutated genes = 37
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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 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.