This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 10 different clustering approaches and 8 clinical features across 587 patients, 5 significant findings detected with P value < 0.05 and Q value < 0.25.
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CNMF clustering analysis on array-based mRNA expression data identified 4 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on array-based mRNA expression data identified 4 subtypes that correlate to 'Time to Death' and 'AGE'.
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CNMF clustering analysis on array-based miR expression data identified 4 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on array-based miR expression data identified 3 subtypes that do not correlate to any clinical features.
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3 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes correlate to 'AGE'.
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3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'Time to Death' and 'AGE'.
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CNMF clustering analysis on RPPA data identified 4 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on RPPA data identified 3 subtypes that do not correlate to any clinical features.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that do not correlate to any clinical features.
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
RACE | ETHNICITY |
Statistical Tests | logrank test | Kruskal-Wallis (anova) | Fisher's exact test | Kruskal-Wallis (anova) | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test |
mRNA CNMF subtypes |
0.0583 (1.00) |
0.0788 (1.00) |
0.4 (1.00) |
0.6 (1.00) |
0.00428 (0.321) |
0.0863 (1.00) |
0.832 (1.00) |
0.124 (1.00) |
mRNA cHierClus subtypes |
0.000563 (0.0434) |
0.00252 (0.191) |
0.0936 (1.00) |
0.509 (1.00) |
0.0302 (1.00) |
0.0166 (1.00) |
0.589 (1.00) |
0.681 (1.00) |
miR CNMF subtypes |
0.00681 (0.497) |
0.38 (1.00) |
0.652 (1.00) |
0.882 (1.00) |
0.359 (1.00) |
0.448 (1.00) |
0.205 (1.00) |
0.855 (1.00) |
miR cHierClus subtypes |
0.312 (1.00) |
0.127 (1.00) |
0.153 (1.00) |
0.571 (1.00) |
0.282 (1.00) |
0.985 (1.00) |
0.191 (1.00) |
0.673 (1.00) |
Copy Number Ratio CNMF subtypes |
0.0305 (1.00) |
2.72e-05 (0.00217) |
0.416 (1.00) |
0.152 (1.00) |
0.144 (1.00) |
0.191 (1.00) |
0.121 (1.00) |
0.761 (1.00) |
METHLYATION CNMF |
0.00018 (0.0141) |
8.57e-05 (0.00677) |
0.601 (1.00) |
0.0612 (1.00) |
0.299 (1.00) |
0.168 (1.00) |
0.992 (1.00) |
0.894 (1.00) |
RPPA CNMF subtypes |
0.327 (1.00) |
0.599 (1.00) |
0.231 (1.00) |
0.459 (1.00) |
0.504 (1.00) |
0.303 (1.00) |
0.704 (1.00) |
1 (1.00) |
RPPA cHierClus subtypes |
0.00439 (0.325) |
0.28 (1.00) |
0.543 (1.00) |
0.0413 (1.00) |
1 (1.00) |
0.242 (1.00) |
0.755 (1.00) |
1 (1.00) |
RNAseq CNMF subtypes |
0.175 (1.00) |
0.0964 (1.00) |
0.0724 (1.00) |
0.67 (1.00) |
0.79 (1.00) |
0.836 (1.00) |
0.793 (1.00) |
0.788 (1.00) |
RNAseq cHierClus subtypes |
0.0268 (1.00) |
0.0784 (1.00) |
0.145 (1.00) |
0.485 (1.00) |
0.604 (1.00) |
0.576 (1.00) |
0.578 (1.00) |
0.735 (1.00) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 154 | 97 | 156 | 118 |
P value = 0.0583 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 525 | 445 | 0.1 - 127.6 (10.4) |
subtype1 | 154 | 138 | 0.1 - 127.6 (9.2) |
subtype2 | 97 | 79 | 0.2 - 108.8 (10.7) |
subtype3 | 156 | 129 | 0.1 - 92.7 (11.5) |
subtype4 | 118 | 99 | 0.2 - 91.8 (9.8) |
P value = 0.0788 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 525 | 57.7 (14.6) |
subtype1 | 154 | 58.4 (12.4) |
subtype2 | 97 | 54.2 (17.4) |
subtype3 | 156 | 60.0 (13.3) |
subtype4 | 118 | 56.5 (15.7) |
P value = 0.4 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 205 | 320 |
subtype1 | 59 | 95 |
subtype2 | 41 | 56 |
subtype3 | 66 | 90 |
subtype4 | 39 | 79 |
P value = 0.6 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 392 | 77.2 (14.4) |
subtype1 | 114 | 78.0 (15.5) |
subtype2 | 75 | 76.5 (11.0) |
subtype3 | 119 | 76.5 (15.2) |
subtype4 | 84 | 77.9 (14.5) |
P value = 0.00428 (Fisher's exact test), Q value = 0.32
nPatients | GLIOBLASTOMA MULTIFORME (GBM) | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|
ALL | 6 | 20 | 499 |
subtype1 | 1 | 8 | 145 |
subtype2 | 0 | 7 | 90 |
subtype3 | 0 | 4 | 152 |
subtype4 | 5 | 1 | 112 |
P value = 0.0863 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 359 | 166 |
subtype1 | 106 | 48 |
subtype2 | 68 | 29 |
subtype3 | 115 | 41 |
subtype4 | 70 | 48 |
P value = 0.832 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 13 | 31 | 462 |
subtype1 | 4 | 12 | 135 |
subtype2 | 2 | 7 | 84 |
subtype3 | 5 | 7 | 139 |
subtype4 | 2 | 5 | 104 |
P value = 0.124 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 438 |
subtype1 | 3 | 131 |
subtype2 | 5 | 68 |
subtype3 | 3 | 135 |
subtype4 | 1 | 104 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 153 | 107 | 103 | 162 |
P value = 0.000563 (logrank test), Q value = 0.043
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 525 | 445 | 0.1 - 127.6 (10.4) |
subtype1 | 153 | 137 | 0.1 - 91.0 (10.6) |
subtype2 | 107 | 80 | 0.2 - 108.8 (10.9) |
subtype3 | 103 | 87 | 0.1 - 92.7 (11.3) |
subtype4 | 162 | 141 | 0.1 - 127.6 (8.9) |
P value = 0.00252 (Kruskal-Wallis (anova)), Q value = 0.19
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 525 | 57.7 (14.6) |
subtype1 | 153 | 56.9 (13.6) |
subtype2 | 107 | 52.9 (17.9) |
subtype3 | 103 | 60.6 (12.1) |
subtype4 | 162 | 59.8 (13.7) |
P value = 0.0936 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 205 | 320 |
subtype1 | 51 | 102 |
subtype2 | 44 | 63 |
subtype3 | 50 | 53 |
subtype4 | 60 | 102 |
P value = 0.509 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 392 | 77.2 (14.4) |
subtype1 | 117 | 78.5 (14.9) |
subtype2 | 83 | 77.6 (11.4) |
subtype3 | 81 | 75.4 (15.5) |
subtype4 | 111 | 76.9 (14.9) |
P value = 0.0302 (Fisher's exact test), Q value = 1
nPatients | GLIOBLASTOMA MULTIFORME (GBM) | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|
ALL | 6 | 20 | 499 |
subtype1 | 0 | 11 | 142 |
subtype2 | 1 | 3 | 103 |
subtype3 | 0 | 3 | 100 |
subtype4 | 5 | 3 | 154 |
P value = 0.0166 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 359 | 166 |
subtype1 | 113 | 40 |
subtype2 | 78 | 29 |
subtype3 | 73 | 30 |
subtype4 | 95 | 67 |
P value = 0.589 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 13 | 31 | 462 |
subtype1 | 4 | 13 | 130 |
subtype2 | 4 | 6 | 95 |
subtype3 | 3 | 4 | 93 |
subtype4 | 2 | 8 | 144 |
P value = 0.681 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 438 |
subtype1 | 5 | 124 |
subtype2 | 1 | 91 |
subtype3 | 2 | 90 |
subtype4 | 4 | 133 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 165 | 182 | 90 | 124 |
P value = 0.00681 (logrank test), Q value = 0.5
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 561 | 461 | 0.1 - 127.6 (10.3) |
subtype1 | 165 | 140 | 0.1 - 91.0 (10.3) |
subtype2 | 182 | 146 | 0.1 - 127.6 (10.4) |
subtype3 | 90 | 72 | 0.1 - 53.8 (8.4) |
subtype4 | 124 | 103 | 0.1 - 92.7 (11.7) |
P value = 0.38 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 561 | 57.9 (14.3) |
subtype1 | 165 | 59.8 (11.6) |
subtype2 | 182 | 55.7 (16.6) |
subtype3 | 90 | 58.5 (14.6) |
subtype4 | 124 | 58.1 (13.6) |
P value = 0.652 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 218 | 343 |
subtype1 | 63 | 102 |
subtype2 | 76 | 106 |
subtype3 | 36 | 54 |
subtype4 | 43 | 81 |
P value = 0.882 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 424 | 77.5 (14.5) |
subtype1 | 127 | 76.6 (15.3) |
subtype2 | 131 | 77.3 (14.6) |
subtype3 | 73 | 78.2 (13.6) |
subtype4 | 93 | 78.4 (14.2) |
P value = 0.359 (Fisher's exact test), Q value = 1
nPatients | GLIOBLASTOMA MULTIFORME (GBM) | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|
ALL | 9 | 20 | 532 |
subtype1 | 2 | 4 | 159 |
subtype2 | 1 | 8 | 173 |
subtype3 | 3 | 5 | 82 |
subtype4 | 3 | 3 | 118 |
P value = 0.448 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 388 | 173 |
subtype1 | 117 | 48 |
subtype2 | 131 | 51 |
subtype3 | 57 | 33 |
subtype4 | 83 | 41 |
P value = 0.205 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 13 | 30 | 493 |
subtype1 | 3 | 13 | 140 |
subtype2 | 7 | 9 | 157 |
subtype3 | 1 | 1 | 85 |
subtype4 | 2 | 7 | 111 |
P value = 0.855 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 459 |
subtype1 | 5 | 134 |
subtype2 | 4 | 153 |
subtype3 | 1 | 71 |
subtype4 | 2 | 101 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 302 | 129 | 130 |
P value = 0.312 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 561 | 461 | 0.1 - 127.6 (10.3) |
subtype1 | 302 | 248 | 0.1 - 108.8 (10.4) |
subtype2 | 129 | 106 | 0.1 - 92.7 (9.6) |
subtype3 | 130 | 107 | 0.1 - 127.6 (9.9) |
P value = 0.127 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 561 | 57.9 (14.3) |
subtype1 | 302 | 56.5 (15.9) |
subtype2 | 129 | 59.0 (11.5) |
subtype3 | 130 | 60.0 (12.5) |
P value = 0.153 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 218 | 343 |
subtype1 | 110 | 192 |
subtype2 | 48 | 81 |
subtype3 | 60 | 70 |
P value = 0.571 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 424 | 77.5 (14.5) |
subtype1 | 225 | 78.4 (13.6) |
subtype2 | 100 | 76.9 (15.4) |
subtype3 | 99 | 76.0 (15.6) |
P value = 0.282 (Fisher's exact test), Q value = 1
nPatients | GLIOBLASTOMA MULTIFORME (GBM) | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|
ALL | 9 | 20 | 532 |
subtype1 | 6 | 13 | 283 |
subtype2 | 3 | 2 | 124 |
subtype3 | 0 | 5 | 125 |
P value = 0.985 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 388 | 173 |
subtype1 | 208 | 94 |
subtype2 | 89 | 40 |
subtype3 | 91 | 39 |
P value = 0.191 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 13 | 30 | 493 |
subtype1 | 7 | 10 | 272 |
subtype2 | 3 | 11 | 113 |
subtype3 | 3 | 9 | 108 |
P value = 0.673 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 459 |
subtype1 | 6 | 249 |
subtype2 | 2 | 109 |
subtype3 | 4 | 101 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 159 | 215 | 191 |
P value = 0.0305 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 565 | 462 | 0.1 - 127.6 (10.0) |
subtype1 | 159 | 137 | 0.1 - 127.6 (9.3) |
subtype2 | 215 | 176 | 0.1 - 77.7 (10.6) |
subtype3 | 191 | 149 | 0.2 - 108.8 (10.5) |
P value = 2.72e-05 (Kruskal-Wallis (anova)), Q value = 0.0022
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 565 | 57.8 (14.5) |
subtype1 | 159 | 60.4 (13.6) |
subtype2 | 215 | 60.0 (10.7) |
subtype3 | 191 | 53.0 (17.5) |
P value = 0.416 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 222 | 343 |
subtype1 | 69 | 90 |
subtype2 | 79 | 136 |
subtype3 | 74 | 117 |
P value = 0.152 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 419 | 77.5 (14.7) |
subtype1 | 114 | 75.8 (14.4) |
subtype2 | 164 | 77.8 (15.4) |
subtype3 | 141 | 78.5 (14.0) |
P value = 0.144 (Fisher's exact test), Q value = 1
nPatients | GLIOBLASTOMA MULTIFORME (GBM) | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|
ALL | 22 | 18 | 525 |
subtype1 | 3 | 4 | 152 |
subtype2 | 7 | 5 | 203 |
subtype3 | 12 | 9 | 170 |
P value = 0.191 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 381 | 184 |
subtype1 | 98 | 61 |
subtype2 | 150 | 65 |
subtype3 | 133 | 58 |
P value = 0.121 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 13 | 44 | 485 |
subtype1 | 1 | 13 | 139 |
subtype2 | 3 | 15 | 188 |
subtype3 | 9 | 16 | 158 |
P value = 0.761 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 467 |
subtype1 | 2 | 132 |
subtype2 | 5 | 174 |
subtype3 | 5 | 161 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 92 | 110 | 81 |
P value = 0.00018 (logrank test), Q value = 0.014
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 283 | 226 | 0.1 - 127.6 (10.6) |
subtype1 | 92 | 72 | 0.1 - 92.7 (9.8) |
subtype2 | 110 | 94 | 0.1 - 77.7 (9.6) |
subtype3 | 81 | 60 | 0.2 - 127.6 (14.0) |
P value = 8.57e-05 (Kruskal-Wallis (anova)), Q value = 0.0068
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 283 | 57.8 (15.0) |
subtype1 | 92 | 59.0 (12.9) |
subtype2 | 110 | 61.8 (12.6) |
subtype3 | 81 | 51.1 (17.8) |
P value = 0.601 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 115 | 168 |
subtype1 | 41 | 51 |
subtype2 | 44 | 66 |
subtype3 | 30 | 51 |
P value = 0.0612 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 214 | 75.4 (15.0) |
subtype1 | 71 | 76.8 (17.0) |
subtype2 | 80 | 73.0 (14.6) |
subtype3 | 63 | 77.0 (12.7) |
P value = 0.299 (Fisher's exact test), Q value = 1
nPatients | GLIOBLASTOMA MULTIFORME (GBM) | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|
ALL | 3 | 19 | 261 |
subtype1 | 3 | 6 | 83 |
subtype2 | 0 | 7 | 103 |
subtype3 | 0 | 6 | 75 |
P value = 0.168 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 210 | 73 |
subtype1 | 73 | 19 |
subtype2 | 75 | 35 |
subtype3 | 62 | 19 |
P value = 0.992 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 10 | 16 | 254 |
subtype1 | 3 | 6 | 82 |
subtype2 | 4 | 6 | 98 |
subtype3 | 3 | 4 | 74 |
P value = 0.894 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 7 | 232 |
subtype1 | 3 | 80 |
subtype2 | 2 | 88 |
subtype3 | 2 | 64 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 57 | 61 | 44 | 49 |
P value = 0.327 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 211 | 159 | 0.1 - 108.8 (8.2) |
subtype1 | 57 | 47 | 0.1 - 53.2 (8.7) |
subtype2 | 61 | 44 | 0.2 - 108.8 (7.7) |
subtype3 | 44 | 31 | 0.1 - 46.2 (9.3) |
subtype4 | 49 | 37 | 0.2 - 47.9 (6.2) |
P value = 0.599 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 211 | 59.9 (14.1) |
subtype1 | 57 | 59.2 (13.6) |
subtype2 | 61 | 57.2 (16.8) |
subtype3 | 44 | 61.5 (12.2) |
subtype4 | 49 | 62.5 (12.0) |
P value = 0.231 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 85 | 126 |
subtype1 | 17 | 40 |
subtype2 | 26 | 35 |
subtype3 | 18 | 26 |
subtype4 | 24 | 25 |
P value = 0.459 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 169 | 75.7 (15.3) |
subtype1 | 46 | 75.0 (15.9) |
subtype2 | 51 | 76.7 (16.5) |
subtype3 | 32 | 78.8 (11.3) |
subtype4 | 40 | 72.8 (15.8) |
P value = 0.504 (Fisher's exact test), Q value = 1
nPatients | GLIOBLASTOMA MULTIFORME (GBM) | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|
ALL | 1 | 3 | 207 |
subtype1 | 0 | 2 | 55 |
subtype2 | 1 | 0 | 60 |
subtype3 | 0 | 0 | 44 |
subtype4 | 0 | 1 | 48 |
P value = 0.303 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 156 | 55 |
subtype1 | 42 | 15 |
subtype2 | 44 | 17 |
subtype3 | 37 | 7 |
subtype4 | 33 | 16 |
P value = 0.704 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 4 | 11 | 180 |
subtype1 | 1 | 4 | 50 |
subtype2 | 2 | 1 | 52 |
subtype3 | 1 | 3 | 38 |
subtype4 | 0 | 3 | 40 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 2 | 177 |
subtype1 | 1 | 48 |
subtype2 | 1 | 52 |
subtype3 | 0 | 39 |
subtype4 | 0 | 38 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 72 | 82 | 57 |
P value = 0.00439 (logrank test), Q value = 0.33
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 211 | 159 | 0.1 - 108.8 (8.2) |
subtype1 | 72 | 58 | 0.2 - 53.2 (6.9) |
subtype2 | 82 | 57 | 0.1 - 108.8 (7.9) |
subtype3 | 57 | 44 | 0.1 - 47.9 (9.4) |
P value = 0.28 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 211 | 59.9 (14.1) |
subtype1 | 72 | 60.9 (13.9) |
subtype2 | 82 | 57.5 (15.4) |
subtype3 | 57 | 62.0 (11.8) |
P value = 0.543 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 85 | 126 |
subtype1 | 27 | 45 |
subtype2 | 37 | 45 |
subtype3 | 21 | 36 |
P value = 0.0413 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 169 | 75.7 (15.3) |
subtype1 | 56 | 71.2 (17.3) |
subtype2 | 69 | 77.5 (13.8) |
subtype3 | 44 | 78.4 (14.0) |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | GLIOBLASTOMA MULTIFORME (GBM) | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|
ALL | 1 | 3 | 207 |
subtype1 | 0 | 1 | 71 |
subtype2 | 1 | 1 | 80 |
subtype3 | 0 | 1 | 56 |
P value = 0.242 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 156 | 55 |
subtype1 | 48 | 24 |
subtype2 | 63 | 19 |
subtype3 | 45 | 12 |
P value = 0.755 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 4 | 11 | 180 |
subtype1 | 1 | 4 | 59 |
subtype2 | 1 | 3 | 73 |
subtype3 | 2 | 4 | 48 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 2 | 177 |
subtype1 | 1 | 56 |
subtype2 | 1 | 72 |
subtype3 | 0 | 49 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 47 | 70 | 35 |
P value = 0.175 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 152 | 117 | 0.2 - 54.0 (9.1) |
subtype1 | 47 | 33 | 0.2 - 54.0 (8.9) |
subtype2 | 70 | 55 | 0.9 - 47.9 (10.1) |
subtype3 | 35 | 29 | 0.2 - 31.3 (6.0) |
P value = 0.0964 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 152 | 59.7 (13.5) |
subtype1 | 47 | 55.6 (16.6) |
subtype2 | 70 | 62.0 (10.6) |
subtype3 | 35 | 60.9 (13.3) |
P value = 0.0724 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 53 | 99 |
subtype1 | 14 | 33 |
subtype2 | 31 | 39 |
subtype3 | 8 | 27 |
P value = 0.67 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 113 | 75.8 (14.4) |
subtype1 | 36 | 74.2 (15.2) |
subtype2 | 51 | 75.7 (14.2) |
subtype3 | 26 | 78.1 (13.9) |
P value = 0.79 (Fisher's exact test), Q value = 1
nPatients | GLIOBLASTOMA MULTIFORME (GBM) | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|
ALL | 1 | 1 | 150 |
subtype1 | 1 | 0 | 46 |
subtype2 | 0 | 1 | 69 |
subtype3 | 0 | 0 | 35 |
P value = 0.836 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 102 | 50 |
subtype1 | 32 | 15 |
subtype2 | 48 | 22 |
subtype3 | 22 | 13 |
P value = 0.793 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 5 | 10 | 136 |
subtype1 | 2 | 3 | 42 |
subtype2 | 1 | 5 | 63 |
subtype3 | 2 | 2 | 31 |
P value = 0.788 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 3 | 125 |
subtype1 | 1 | 44 |
subtype2 | 2 | 51 |
subtype3 | 0 | 30 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 32 | 96 | 24 |
P value = 0.0268 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 152 | 117 | 0.2 - 54.0 (9.1) |
subtype1 | 32 | 22 | 0.2 - 54.0 (11.7) |
subtype2 | 96 | 75 | 0.4 - 47.9 (9.1) |
subtype3 | 24 | 20 | 0.2 - 30.6 (5.7) |
P value = 0.0784 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 152 | 59.7 (13.5) |
subtype1 | 32 | 54.2 (18.3) |
subtype2 | 96 | 61.6 (11.4) |
subtype3 | 24 | 59.6 (12.5) |
P value = 0.145 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 53 | 99 |
subtype1 | 9 | 23 |
subtype2 | 39 | 57 |
subtype3 | 5 | 19 |
P value = 0.485 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 113 | 75.8 (14.4) |
subtype1 | 24 | 77.1 (11.6) |
subtype2 | 73 | 74.5 (14.7) |
subtype3 | 16 | 79.4 (16.5) |
P value = 0.604 (Fisher's exact test), Q value = 1
nPatients | GLIOBLASTOMA MULTIFORME (GBM) | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|
ALL | 1 | 1 | 150 |
subtype1 | 1 | 0 | 31 |
subtype2 | 0 | 1 | 95 |
subtype3 | 0 | 0 | 24 |
P value = 0.576 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 102 | 50 |
subtype1 | 24 | 8 |
subtype2 | 62 | 34 |
subtype3 | 16 | 8 |
P value = 0.578 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 5 | 10 | 136 |
subtype1 | 2 | 1 | 29 |
subtype2 | 2 | 8 | 85 |
subtype3 | 1 | 1 | 22 |
P value = 0.735 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 3 | 125 |
subtype1 | 0 | 30 |
subtype2 | 3 | 75 |
subtype3 | 0 | 20 |
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Cluster data file = GBM-TP.mergedcluster.txt
-
Clinical data file = GBM-TP.merged_data.txt
-
Number of patients = 587
-
Number of clustering approaches = 10
-
Number of selected clinical features = 8
-
Exclude small clusters that include fewer than K patients, K = 3
consensus non-negative matrix factorization clustering approach (Brunet et al. 2004)
Resampling-based clustering method (Monti et al. 2003)
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For binary clinical features, 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.