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 6 clinical features across 575 patients, 2 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 correlate to 'HISTOLOGICAL.TYPE'.
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Consensus hierarchical clustering analysis on array-based mRNA expression data identified 3 subtypes that do not correlate to any clinical features.
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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 do not correlate to any clinical features.
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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 |
Statistical Tests | logrank test | ANOVA | Fisher's exact test | ANOVA | Chi-square test | Fisher's exact test |
mRNA CNMF subtypes |
0.0517 (1.00) |
0.013 (0.716) |
0.399 (1.00) |
0.861 (1.00) |
0.0024 (0.142) |
0.0689 (1.00) |
mRNA cHierClus subtypes |
0.0944 (1.00) |
0.0808 (1.00) |
0.611 (1.00) |
0.806 (1.00) |
0.0746 (1.00) |
0.182 (1.00) |
miR CNMF subtypes |
0.00437 (0.253) |
0.0648 (1.00) |
0.68 (1.00) |
0.85 (1.00) |
0.431 (1.00) |
0.441 (1.00) |
miR cHierClus subtypes |
0.355 (1.00) |
0.056 (1.00) |
0.0302 (1.00) |
0.978 (1.00) |
0.0375 (1.00) |
0.934 (1.00) |
Copy Number Ratio CNMF subtypes |
0.00779 (0.444) |
4.64e-07 (2.78e-05) |
0.514 (1.00) |
0.946 (1.00) |
0.0118 (0.66) |
0.602 (1.00) |
METHLYATION CNMF |
0.577 (1.00) |
0.115 (1.00) |
0.406 (1.00) |
0.722 (1.00) |
0.661 (1.00) |
0.475 (1.00) |
RPPA CNMF subtypes |
0.272 (1.00) |
0.233 (1.00) |
0.222 (1.00) |
0.403 (1.00) |
0.439 (1.00) |
0.313 (1.00) |
RPPA cHierClus subtypes |
0.281 (1.00) |
0.46 (1.00) |
0.625 (1.00) |
0.695 (1.00) |
0.743 (1.00) |
0.49 (1.00) |
RNAseq CNMF subtypes |
0.224 (1.00) |
0.0368 (1.00) |
0.0673 (1.00) |
0.576 (1.00) |
0.491 (1.00) |
0.833 (1.00) |
RNAseq cHierClus subtypes |
0.656 (1.00) |
0.0255 (1.00) |
0.0877 (1.00) |
0.32 (1.00) |
0.115 (1.00) |
0.887 (1.00) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 154 | 97 | 156 | 118 |
P value = 0.0517 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 525 | 433 | 0.1 - 127.6 (10.4) |
subtype1 | 154 | 136 | 0.1 - 127.6 (9.2) |
subtype2 | 97 | 76 | 0.2 - 108.8 (10.6) |
subtype3 | 156 | 123 | 0.1 - 92.6 (11.3) |
subtype4 | 118 | 98 | 0.2 - 91.7 (9.8) |
P value = 0.013 (ANOVA), Q value = 0.72
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 = 0.399 (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 = 0.861 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 389 | 77.1 (14.4) |
subtype1 | 113 | 77.9 (15.5) |
subtype2 | 75 | 76.5 (11.0) |
subtype3 | 119 | 76.5 (15.2) |
subtype4 | 82 | 77.6 (14.5) |
P value = 0.0024 (Chi-square test), Q value = 0.14
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 = 0.0689 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 360 | 165 |
subtype1 | 106 | 48 |
subtype2 | 68 | 29 |
subtype3 | 116 | 40 |
subtype4 | 70 | 48 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 119 | 177 | 229 |
P value = 0.0944 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 525 | 433 | 0.1 - 127.6 (10.4) |
subtype1 | 119 | 95 | 0.1 - 92.6 (11.2) |
subtype2 | 177 | 144 | 0.2 - 127.6 (9.9) |
subtype3 | 229 | 194 | 0.1 - 91.0 (10.0) |
P value = 0.0808 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 525 | 57.7 (14.6) |
subtype1 | 119 | 59.9 (13.8) |
subtype2 | 177 | 56.0 (16.2) |
subtype3 | 229 | 57.8 (13.5) |
P value = 0.611 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 205 | 320 |
subtype1 | 49 | 70 |
subtype2 | 64 | 113 |
subtype3 | 92 | 137 |
P value = 0.806 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 389 | 77.1 (14.4) |
subtype1 | 92 | 76.6 (15.9) |
subtype2 | 127 | 77.8 (11.9) |
subtype3 | 170 | 76.9 (15.2) |
P value = 0.0746 (Chi-square test), Q value = 1
nPatients | GLIOBLASTOMA MULTIFORME (GBM) | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|
ALL | 6 | 20 | 499 |
subtype1 | 0 | 5 | 114 |
subtype2 | 5 | 4 | 168 |
subtype3 | 1 | 11 | 217 |
P value = 0.182 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 360 | 165 |
subtype1 | 85 | 34 |
subtype2 | 112 | 65 |
subtype3 | 163 | 66 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 165 | 182 | 90 | 123 |
P value = 0.00437 (logrank test), Q value = 0.25
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 560 | 448 | 0.1 - 127.6 (9.9) |
subtype1 | 165 | 136 | 0.1 - 91.0 (10.3) |
subtype2 | 182 | 141 | 0.1 - 127.6 (10.4) |
subtype3 | 90 | 72 | 0.1 - 53.8 (8.4) |
subtype4 | 123 | 99 | 0.1 - 92.6 (11.5) |
P value = 0.0648 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 560 | 57.9 (14.3) |
subtype1 | 165 | 59.8 (11.6) |
subtype2 | 182 | 55.7 (16.6) |
subtype3 | 90 | 58.5 (14.6) |
subtype4 | 123 | 58.2 (13.7) |
P value = 0.68 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 218 | 342 |
subtype1 | 63 | 102 |
subtype2 | 76 | 106 |
subtype3 | 36 | 54 |
subtype4 | 43 | 80 |
P value = 0.85 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 419 | 77.4 (14.6) |
subtype1 | 125 | 76.6 (15.4) |
subtype2 | 131 | 77.3 (14.6) |
subtype3 | 72 | 78.1 (13.6) |
subtype4 | 91 | 78.1 (14.2) |
P value = 0.431 (Chi-square test), Q value = 1
nPatients | GLIOBLASTOMA MULTIFORME (GBM) | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|
ALL | 8 | 20 | 532 |
subtype1 | 2 | 4 | 159 |
subtype2 | 1 | 8 | 173 |
subtype3 | 3 | 5 | 82 |
subtype4 | 2 | 3 | 118 |
P value = 0.441 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 389 | 171 |
subtype1 | 118 | 47 |
subtype2 | 131 | 51 |
subtype3 | 57 | 33 |
subtype4 | 83 | 40 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 178 | 188 | 194 |
P value = 0.355 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 560 | 448 | 0.1 - 127.6 (9.9) |
subtype1 | 178 | 139 | 0.1 - 127.6 (10.3) |
subtype2 | 188 | 148 | 0.1 - 108.8 (9.4) |
subtype3 | 194 | 161 | 0.1 - 92.6 (10.3) |
P value = 0.056 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 560 | 57.9 (14.3) |
subtype1 | 178 | 58.6 (13.5) |
subtype2 | 188 | 55.9 (16.4) |
subtype3 | 194 | 59.2 (12.7) |
P value = 0.0302 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 218 | 342 |
subtype1 | 83 | 95 |
subtype2 | 70 | 118 |
subtype3 | 65 | 129 |
P value = 0.978 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 419 | 77.4 (14.6) |
subtype1 | 133 | 77.5 (15.5) |
subtype2 | 141 | 77.4 (14.3) |
subtype3 | 145 | 77.2 (14.1) |
P value = 0.0375 (Chi-square test), Q value = 1
nPatients | GLIOBLASTOMA MULTIFORME (GBM) | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|
ALL | 8 | 20 | 532 |
subtype1 | 0 | 9 | 169 |
subtype2 | 5 | 9 | 174 |
subtype3 | 3 | 2 | 189 |
P value = 0.934 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 389 | 171 |
subtype1 | 125 | 53 |
subtype2 | 131 | 57 |
subtype3 | 133 | 61 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 149 | 219 | 185 |
P value = 0.00779 (logrank test), Q value = 0.44
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 553 | 445 | 0.1 - 127.6 (9.9) |
subtype1 | 149 | 124 | 0.1 - 92.6 (9.3) |
subtype2 | 219 | 177 | 0.1 - 77.6 (10.4) |
subtype3 | 185 | 144 | 0.2 - 127.6 (10.6) |
P value = 4.64e-07 (ANOVA), Q value = 2.8e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 553 | 57.8 (14.4) |
subtype1 | 149 | 59.8 (14.2) |
subtype2 | 219 | 60.4 (10.9) |
subtype3 | 185 | 53.2 (17.0) |
P value = 0.514 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 218 | 335 |
subtype1 | 64 | 85 |
subtype2 | 81 | 138 |
subtype3 | 73 | 112 |
P value = 0.946 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 408 | 77.4 (14.7) |
subtype1 | 106 | 77.0 (14.2) |
subtype2 | 170 | 77.6 (15.4) |
subtype3 | 132 | 77.3 (14.4) |
P value = 0.0118 (Chi-square test), Q value = 0.66
nPatients | GLIOBLASTOMA MULTIFORME (GBM) | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|
ALL | 10 | 18 | 525 |
subtype1 | 0 | 4 | 145 |
subtype2 | 2 | 5 | 212 |
subtype3 | 8 | 9 | 168 |
P value = 0.602 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 382 | 171 |
subtype1 | 98 | 51 |
subtype2 | 154 | 65 |
subtype3 | 130 | 55 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 32 | 44 | 32 |
P value = 0.577 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 108 | 58 | 0.1 - 58.8 (7.4) |
subtype1 | 32 | 17 | 0.8 - 58.8 (5.8) |
subtype2 | 44 | 26 | 0.1 - 47.9 (8.0) |
subtype3 | 32 | 15 | 1.2 - 50.5 (7.6) |
P value = 0.115 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 108 | 60.9 (12.0) |
subtype1 | 32 | 60.2 (13.8) |
subtype2 | 44 | 63.6 (8.4) |
subtype3 | 32 | 57.8 (13.8) |
P value = 0.406 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 47 | 61 |
subtype1 | 12 | 20 |
subtype2 | 18 | 26 |
subtype3 | 17 | 15 |
P value = 0.722 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 76.5 (15.2) |
subtype1 | 22 | 77.7 (18.0) |
subtype2 | 33 | 74.8 (15.6) |
subtype3 | 25 | 77.6 (12.0) |
P value = 0.661 (Chi-square test), Q value = 1
nPatients | GLIOBLASTOMA MULTIFORME (GBM) | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|
ALL | 2 | 1 | 105 |
subtype1 | 0 | 0 | 32 |
subtype2 | 1 | 1 | 42 |
subtype3 | 1 | 0 | 31 |
P value = 0.475 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 78 | 30 |
subtype1 | 25 | 7 |
subtype2 | 29 | 15 |
subtype3 | 24 | 8 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 57 | 60 | 44 | 49 |
P value = 0.272 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 210 | 150 | 0.1 - 108.8 (8.1) |
subtype1 | 57 | 46 | 0.1 - 53.2 (8.7) |
subtype2 | 60 | 40 | 0.2 - 108.8 (7.4) |
subtype3 | 44 | 29 | 0.1 - 46.2 (9.3) |
subtype4 | 49 | 35 | 0.2 - 47.9 (6.1) |
P value = 0.233 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 210 | 59.9 (14.1) |
subtype1 | 57 | 59.2 (13.6) |
subtype2 | 60 | 57.4 (16.9) |
subtype3 | 44 | 61.5 (12.2) |
subtype4 | 49 | 62.5 (12.0) |
P value = 0.222 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 85 | 125 |
subtype1 | 17 | 40 |
subtype2 | 26 | 34 |
subtype3 | 18 | 26 |
subtype4 | 24 | 25 |
P value = 0.403 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 168 | 75.6 (15.3) |
subtype1 | 46 | 75.0 (15.9) |
subtype2 | 50 | 76.4 (16.5) |
subtype3 | 32 | 78.8 (11.3) |
subtype4 | 40 | 72.8 (15.8) |
P value = 0.439 (Fisher's exact test), Q value = 1
nPatients | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|
ALL | 3 | 207 |
subtype1 | 2 | 55 |
subtype2 | 0 | 60 |
subtype3 | 0 | 44 |
subtype4 | 1 | 48 |
P value = 0.313 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 156 | 54 |
subtype1 | 42 | 15 |
subtype2 | 44 | 16 |
subtype3 | 37 | 7 |
subtype4 | 33 | 16 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 64 | 35 | 111 |
P value = 0.281 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 210 | 150 | 0.1 - 108.8 (8.1) |
subtype1 | 64 | 45 | 0.1 - 47.9 (9.2) |
subtype2 | 35 | 29 | 0.3 - 53.2 (7.9) |
subtype3 | 111 | 76 | 0.2 - 108.8 (6.7) |
P value = 0.46 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 210 | 59.9 (14.1) |
subtype1 | 64 | 61.7 (12.1) |
subtype2 | 35 | 58.4 (13.2) |
subtype3 | 111 | 59.4 (15.4) |
P value = 0.625 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 85 | 125 |
subtype1 | 25 | 39 |
subtype2 | 12 | 23 |
subtype3 | 48 | 63 |
P value = 0.695 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 168 | 75.6 (15.3) |
subtype1 | 49 | 76.9 (14.2) |
subtype2 | 26 | 73.8 (17.7) |
subtype3 | 93 | 75.4 (15.3) |
P value = 0.743 (Fisher's exact test), Q value = 1
nPatients | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|
ALL | 3 | 207 |
subtype1 | 1 | 63 |
subtype2 | 1 | 34 |
subtype3 | 1 | 110 |
P value = 0.49 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 156 | 54 |
subtype1 | 51 | 13 |
subtype2 | 26 | 9 |
subtype3 | 79 | 32 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 47 | 70 | 35 |
P value = 0.224 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 152 | 113 | 0.2 - 54.0 (9.1) |
subtype1 | 47 | 33 | 0.2 - 54.0 (8.8) |
subtype2 | 70 | 52 | 0.9 - 47.9 (9.8) |
subtype3 | 35 | 28 | 0.2 - 31.3 (6.0) |
P value = 0.0368 (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 = 0.0673 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 53 | 99 |
subtype1 | 14 | 33 |
subtype2 | 31 | 39 |
subtype3 | 8 | 27 |
P value = 0.576 (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 = 0.491 (Chi-square 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 = 0.833 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 102 | 50 |
subtype1 | 32 | 15 |
subtype2 | 48 | 22 |
subtype3 | 22 | 13 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 69 | 22 | 61 |
P value = 0.656 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 152 | 113 | 0.2 - 54.0 (9.1) |
subtype1 | 69 | 48 | 0.4 - 40.4 (8.8) |
subtype2 | 22 | 19 | 1.1 - 47.9 (10.2) |
subtype3 | 61 | 46 | 0.2 - 54.0 (9.1) |
P value = 0.0255 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 152 | 59.7 (13.5) |
subtype1 | 69 | 62.1 (11.5) |
subtype2 | 22 | 62.3 (10.5) |
subtype3 | 61 | 56.1 (15.8) |
P value = 0.0877 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 53 | 99 |
subtype1 | 29 | 40 |
subtype2 | 9 | 13 |
subtype3 | 15 | 46 |
P value = 0.32 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 113 | 75.8 (14.4) |
subtype1 | 51 | 74.7 (14.6) |
subtype2 | 18 | 72.8 (15.3) |
subtype3 | 44 | 78.2 (13.7) |
P value = 0.115 (Chi-square test), Q value = 1
nPatients | GLIOBLASTOMA MULTIFORME (GBM) | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|
ALL | 1 | 1 | 150 |
subtype1 | 0 | 0 | 69 |
subtype2 | 0 | 1 | 21 |
subtype3 | 1 | 0 | 60 |
P value = 0.887 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 102 | 50 |
subtype1 | 46 | 23 |
subtype2 | 14 | 8 |
subtype3 | 42 | 19 |
-
Cluster data file = GBM-TP.mergedcluster.txt
-
Clinical data file = GBM-TP.merged_data.txt
-
Number of patients = 575
-
Number of clustering approaches = 10
-
Number of selected clinical features = 6
-
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 continuous numerical clinical features, one-way analysis of variance (Howell 2002) was applied to compare the clinical values between tumor subtypes using 'anova' 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 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.