This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 9 different clustering approaches and 7 clinical features across 566 patients, 13 significant findings detected with P value < 0.05.
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CNMF clustering analysis on array-based mRNA expression data identified 3 subtypes that correlate to 'Time to Death' and 'TUMOR.STAGE'.
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Consensus hierarchical clustering analysis on array-based mRNA expression data identified 3 subtypes that correlate to 'Time to Death', 'AGE', 'TUMOR.STAGE', and 'NEOADJUVANT.THERAPY'.
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CNMF clustering analysis on array-based miR expression data identified 3 subtypes that correlate to 'Time to Death'.
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Consensus hierarchical clustering analysis on array-based miR expression data identified 3 subtypes that correlate to 'Time to Death'.
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4 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'AGE'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'AGE' and 'TUMOR.STAGE'.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'TUMOR.STAGE'.
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CNMF clustering analysis on sequencing-based miR expression data identified 3 subtypes that correlate to 'Time to Death'.
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Consensus hierarchical clustering analysis on sequencing-based miR expression data identified 3 subtypes that do not correlate to any clinical features.
Clinical Features |
Time to Death |
AGE |
PRIMARY SITE OF DISEASE |
KARNOFSKY PERFORMANCE SCORE |
TUMOR STAGE |
RADIATIONS RADIATION REGIMENINDICATION |
NEOADJUVANT THERAPY |
Statistical Tests | logrank test | ANOVA | Chi-square test | ANOVA | Chi-square test | Fisher's exact test | Fisher's exact test |
mRNA CNMF subtypes | 0.00933 | 0.06 | 0.555 | 0.147 | 0.031 | 0.793 | 0.371 |
mRNA cHierClus subtypes | 0.00116 | 0.00679 | 0.588 | 0.241 | 0.0228 | 0.619 | 0.0475 |
miR CNMF subtypes | 0.00559 | 0.698 | 0.201 | 0.677 | 0.11 | 0.265 | 0.275 |
miR cHierClus subtypes | 0.0418 | 0.504 | 0.0908 | 0.547 | 0.0541 | 0.533 | 0.641 |
METHLYATION CNMF | 0.251 | 1.3e-11 | 0.656 | 0.509 | 0.0557 | 0.189 | 0.281 |
RNAseq CNMF subtypes | 0.186 | 0.0011 | 0.736 | 0.277 | 0.021 | 0.189 | 0.536 |
RNAseq cHierClus subtypes | 0.139 | 0.108 | 0.615 | 0.273 | 0.0365 | 1 | 0.725 |
MIRseq CNMF subtypes | 0.0121 | 0.594 | 0.0583 | 0.207 | 0.193 | 0.476 | 0.546 |
MIRseq cHierClus subtypes | 0.284 | 0.757 | 0.812 | 0.577 | 0.49 | 0.281 | 0.753 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 225 | 207 | 132 |
P value = 0.00933 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 559 | 292 | 0.3 - 180.2 (28.3) |
subtype1 | 222 | 127 | 0.3 - 152.0 (29.1) |
subtype2 | 205 | 90 | 0.4 - 180.2 (27.9) |
subtype3 | 132 | 75 | 0.3 - 119.1 (26.7) |
P value = 0.06 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 553 | 59.7 (11.6) |
subtype1 | 219 | 61.0 (11.6) |
subtype2 | 203 | 58.4 (11.3) |
subtype3 | 131 | 59.5 (11.9) |
P value = 0.555 (Chi-square test)
nPatients | OMENTUM | OVARY | PERITONEUM (OVARY) |
---|---|---|---|
ALL | 2 | 560 | 2 |
subtype1 | 0 | 225 | 0 |
subtype2 | 1 | 205 | 1 |
subtype3 | 1 | 130 | 1 |
P value = 0.147 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 75.6 (12.8) |
subtype1 | 31 | 78.1 (13.0) |
subtype2 | 27 | 76.3 (12.4) |
subtype3 | 20 | 71.0 (12.1) |
P value = 0.031 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 16 | 26 | 433 | 85 |
subtype1 | 7 | 9 | 178 | 29 |
subtype2 | 9 | 15 | 150 | 32 |
subtype3 | 0 | 2 | 105 | 24 |
P value = 0.793 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 3 | 561 |
subtype1 | 2 | 223 |
subtype2 | 1 | 206 |
subtype3 | 0 | 132 |
P value = 0.371 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 456 | 108 |
subtype1 | 176 | 49 |
subtype2 | 173 | 34 |
subtype3 | 107 | 25 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 209 | 223 | 132 |
P value = 0.00116 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 559 | 292 | 0.3 - 180.2 (28.3) |
subtype1 | 206 | 124 | 0.3 - 152.0 (29.6) |
subtype2 | 221 | 87 | 0.5 - 116.1 (27.5) |
subtype3 | 132 | 81 | 0.3 - 180.2 (27.6) |
P value = 0.00679 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 553 | 59.7 (11.6) |
subtype1 | 202 | 61.7 (11.5) |
subtype2 | 221 | 58.5 (11.0) |
subtype3 | 130 | 58.6 (12.4) |
P value = 0.588 (Chi-square test)
nPatients | OMENTUM | OVARY | PERITONEUM (OVARY) |
---|---|---|---|
ALL | 2 | 560 | 2 |
subtype1 | 0 | 209 | 0 |
subtype2 | 1 | 221 | 1 |
subtype3 | 1 | 130 | 1 |
P value = 0.241 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 75.6 (12.8) |
subtype1 | 25 | 79.2 (13.5) |
subtype2 | 33 | 73.9 (11.7) |
subtype3 | 20 | 74.0 (13.1) |
P value = 0.0228 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 16 | 26 | 433 | 85 |
subtype1 | 7 | 10 | 165 | 25 |
subtype2 | 9 | 15 | 162 | 36 |
subtype3 | 0 | 1 | 106 | 24 |
P value = 0.619 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 3 | 561 |
subtype1 | 2 | 207 |
subtype2 | 1 | 222 |
subtype3 | 0 | 132 |
P value = 0.0475 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 456 | 108 |
subtype1 | 160 | 49 |
subtype2 | 191 | 32 |
subtype3 | 105 | 27 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 159 | 163 | 240 |
P value = 0.00559 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 557 | 292 | 0.3 - 180.2 (28.2) |
subtype1 | 158 | 86 | 0.3 - 130.0 (25.5) |
subtype2 | 160 | 92 | 0.3 - 109.7 (24.7) |
subtype3 | 239 | 114 | 0.3 - 180.2 (30.1) |
P value = 0.698 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 551 | 59.7 (11.6) |
subtype1 | 155 | 59.0 (12.3) |
subtype2 | 160 | 59.8 (11.8) |
subtype3 | 236 | 60.1 (11.1) |
P value = 0.201 (Chi-square test)
nPatients | OMENTUM | OVARY | PERITONEUM (OVARY) |
---|---|---|---|
ALL | 2 | 558 | 2 |
subtype1 | 0 | 157 | 2 |
subtype2 | 1 | 162 | 0 |
subtype3 | 1 | 239 | 0 |
P value = 0.677 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 75.6 (12.8) |
subtype1 | 25 | 76.8 (12.5) |
subtype2 | 22 | 73.6 (15.6) |
subtype3 | 31 | 76.1 (10.9) |
P value = 0.11 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 16 | 25 | 432 | 85 |
subtype1 | 3 | 6 | 115 | 33 |
subtype2 | 7 | 5 | 133 | 17 |
subtype3 | 6 | 14 | 184 | 35 |
P value = 0.265 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 3 | 559 |
subtype1 | 0 | 159 |
subtype2 | 0 | 163 |
subtype3 | 3 | 237 |
P value = 0.275 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 454 | 108 |
subtype1 | 130 | 29 |
subtype2 | 125 | 38 |
subtype3 | 199 | 41 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 200 | 186 | 176 |
P value = 0.0418 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 557 | 292 | 0.3 - 180.2 (28.2) |
subtype1 | 197 | 95 | 0.3 - 180.2 (29.0) |
subtype2 | 184 | 99 | 0.5 - 152.0 (29.0) |
subtype3 | 176 | 98 | 0.3 - 130.0 (24.6) |
P value = 0.504 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 551 | 59.7 (11.6) |
subtype1 | 198 | 60.0 (11.8) |
subtype2 | 181 | 60.2 (11.0) |
subtype3 | 172 | 58.8 (12.2) |
P value = 0.0908 (Chi-square test)
nPatients | OMENTUM | OVARY | PERITONEUM (OVARY) |
---|---|---|---|
ALL | 2 | 558 | 2 |
subtype1 | 2 | 198 | 0 |
subtype2 | 0 | 186 | 0 |
subtype3 | 0 | 174 | 2 |
P value = 0.547 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 75.6 (12.8) |
subtype1 | 31 | 76.1 (13.1) |
subtype2 | 20 | 73.0 (13.4) |
subtype3 | 27 | 77.0 (12.0) |
P value = 0.0541 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 16 | 25 | 432 | 85 |
subtype1 | 4 | 9 | 152 | 33 |
subtype2 | 9 | 10 | 149 | 17 |
subtype3 | 3 | 6 | 131 | 35 |
P value = 0.533 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 3 | 559 |
subtype1 | 1 | 199 |
subtype2 | 2 | 184 |
subtype3 | 0 | 176 |
P value = 0.641 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 454 | 108 |
subtype1 | 164 | 36 |
subtype2 | 146 | 40 |
subtype3 | 144 | 32 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 105 | 137 | 151 | 156 |
P value = 0.251 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 543 | 290 | 0.3 - 180.2 (29.0) |
subtype1 | 102 | 48 | 0.4 - 130.0 (23.5) |
subtype2 | 135 | 78 | 0.8 - 125.7 (29.1) |
subtype3 | 150 | 80 | 0.3 - 180.2 (30.3) |
subtype4 | 156 | 84 | 0.3 - 152.0 (29.4) |
P value = 1.3e-11 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 539 | 59.7 (11.7) |
subtype1 | 104 | 58.3 (12.5) |
subtype2 | 134 | 64.5 (11.0) |
subtype3 | 147 | 54.9 (11.2) |
subtype4 | 154 | 61.1 (10.2) |
P value = 0.656 (Chi-square test)
nPatients | OMENTUM | OVARY | PERITONEUM (OVARY) |
---|---|---|---|
ALL | 2 | 545 | 2 |
subtype1 | 1 | 104 | 0 |
subtype2 | 0 | 136 | 1 |
subtype3 | 0 | 151 | 0 |
subtype4 | 1 | 154 | 1 |
P value = 0.509 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 75.6 (12.8) |
subtype1 | 19 | 72.6 (13.7) |
subtype2 | 19 | 75.8 (15.7) |
subtype3 | 19 | 78.9 (8.1) |
subtype4 | 21 | 75.2 (12.5) |
P value = 0.0557 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 16 | 24 | 421 | 83 |
subtype1 | 2 | 5 | 77 | 19 |
subtype2 | 5 | 4 | 114 | 11 |
subtype3 | 5 | 4 | 109 | 33 |
subtype4 | 4 | 11 | 121 | 20 |
P value = 0.189 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 3 | 546 |
subtype1 | 1 | 104 |
subtype2 | 2 | 135 |
subtype3 | 0 | 151 |
subtype4 | 0 | 156 |
P value = 0.281 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 441 | 108 |
subtype1 | 84 | 21 |
subtype2 | 106 | 31 |
subtype3 | 129 | 22 |
subtype4 | 122 | 34 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 81 | 101 | 115 |
P value = 0.186 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 295 | 169 | 0.3 - 180.2 (28.3) |
subtype1 | 80 | 42 | 1.0 - 116.1 (31.0) |
subtype2 | 100 | 63 | 0.3 - 152.0 (26.4) |
subtype3 | 115 | 64 | 0.4 - 180.2 (27.5) |
P value = 0.0011 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 289 | 59.2 (11.0) |
subtype1 | 79 | 55.5 (10.6) |
subtype2 | 98 | 61.4 (10.7) |
subtype3 | 112 | 59.9 (11.1) |
P value = 0.736 (Fisher's exact test)
nPatients | OMENTUM | OVARY |
---|---|---|
ALL | 2 | 295 |
subtype1 | 1 | 80 |
subtype2 | 0 | 101 |
subtype3 | 1 | 114 |
P value = 0.277 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 16 | 76.2 (13.1) |
subtype1 | 2 | 80.0 (0.0) |
subtype2 | 3 | 80.0 (0.0) |
subtype3 | 11 | 74.5 (15.7) |
P value = 0.021 (Chi-square test)
nPatients | II | III | IV |
---|---|---|---|
ALL | 18 | 241 | 36 |
subtype1 | 9 | 58 | 14 |
subtype2 | 7 | 85 | 8 |
subtype3 | 2 | 98 | 14 |
P value = 0.189 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 2 | 295 |
subtype1 | 0 | 81 |
subtype2 | 2 | 99 |
subtype3 | 0 | 115 |
P value = 0.536 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 241 | 56 |
subtype1 | 63 | 18 |
subtype2 | 85 | 16 |
subtype3 | 93 | 22 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 35 | 115 | 147 |
P value = 0.139 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 295 | 169 | 0.3 - 180.2 (28.3) |
subtype1 | 35 | 24 | 0.3 - 89.3 (28.7) |
subtype2 | 114 | 71 | 0.5 - 152.0 (27.4) |
subtype3 | 146 | 74 | 0.4 - 180.2 (29.0) |
P value = 0.108 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 289 | 59.2 (11.0) |
subtype1 | 34 | 56.3 (10.6) |
subtype2 | 112 | 58.6 (10.6) |
subtype3 | 143 | 60.4 (11.4) |
P value = 0.615 (Fisher's exact test)
nPatients | OMENTUM | OVARY |
---|---|---|
ALL | 2 | 295 |
subtype1 | 0 | 35 |
subtype2 | 0 | 115 |
subtype3 | 2 | 145 |
P value = 0.273 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 16 | 76.2 (13.1) |
subtype2 | 3 | 80.0 (0.0) |
subtype3 | 13 | 75.4 (14.5) |
P value = 0.0365 (Chi-square test)
nPatients | II | III | IV |
---|---|---|---|
ALL | 18 | 241 | 36 |
subtype1 | 2 | 23 | 10 |
subtype2 | 8 | 95 | 11 |
subtype3 | 8 | 123 | 15 |
P value = 1 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 2 | 295 |
subtype1 | 0 | 35 |
subtype2 | 1 | 114 |
subtype3 | 1 | 146 |
P value = 0.725 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 241 | 56 |
subtype1 | 27 | 8 |
subtype2 | 95 | 20 |
subtype3 | 119 | 28 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 113 | 195 | 146 |
P value = 0.0121 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 451 | 252 | 0.3 - 180.2 (30.1) |
subtype1 | 113 | 74 | 0.3 - 152.0 (27.0) |
subtype2 | 194 | 101 | 0.3 - 180.2 (32.5) |
subtype3 | 144 | 77 | 0.3 - 130.0 (28.7) |
P value = 0.594 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 446 | 59.8 (11.5) |
subtype1 | 112 | 60.8 (11.7) |
subtype2 | 192 | 59.5 (11.3) |
subtype3 | 142 | 59.5 (11.6) |
P value = 0.0583 (Chi-square test)
nPatients | OMENTUM | OVARY | PERITONEUM (OVARY) |
---|---|---|---|
ALL | 2 | 451 | 1 |
subtype1 | 2 | 110 | 1 |
subtype2 | 0 | 195 | 0 |
subtype3 | 0 | 146 | 0 |
P value = 0.207 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 64 | 75.3 (13.2) |
subtype1 | 10 | 82.0 (14.8) |
subtype2 | 46 | 74.3 (12.4) |
subtype3 | 8 | 72.5 (14.9) |
P value = 0.193 (Chi-square test)
nPatients | II | III | IV |
---|---|---|---|
ALL | 24 | 352 | 74 |
subtype1 | 4 | 91 | 17 |
subtype2 | 8 | 147 | 38 |
subtype3 | 12 | 114 | 19 |
P value = 0.476 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 3 | 451 |
subtype1 | 0 | 113 |
subtype2 | 1 | 194 |
subtype3 | 2 | 144 |
P value = 0.546 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 367 | 87 |
subtype1 | 89 | 24 |
subtype2 | 162 | 33 |
subtype3 | 116 | 30 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 3 | 153 | 298 |
P value = 0.284 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 451 | 252 | 0.3 - 180.2 (30.1) |
subtype1 | 3 | 3 | 4.5 - 60.6 (33.7) |
subtype2 | 151 | 82 | 0.3 - 130.0 (28.6) |
subtype3 | 297 | 167 | 0.3 - 180.2 (31.0) |
P value = 0.757 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 446 | 59.8 (11.5) |
subtype1 | 3 | 62.7 (1.5) |
subtype2 | 149 | 59.3 (11.9) |
subtype3 | 294 | 60.0 (11.4) |
P value = 0.812 (Chi-square test)
nPatients | OMENTUM | OVARY | PERITONEUM (OVARY) |
---|---|---|---|
ALL | 2 | 451 | 1 |
subtype1 | 0 | 3 | 0 |
subtype2 | 0 | 153 | 0 |
subtype3 | 2 | 295 | 1 |
P value = 0.577 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 64 | 75.3 (13.2) |
subtype2 | 8 | 72.5 (14.9) |
subtype3 | 56 | 75.7 (13.1) |
P value = 0.49 (Chi-square test)
nPatients | II | III | IV |
---|---|---|---|
ALL | 24 | 352 | 74 |
subtype1 | 0 | 3 | 0 |
subtype2 | 11 | 120 | 21 |
subtype3 | 13 | 229 | 53 |
P value = 0.281 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 3 | 451 |
subtype1 | 0 | 3 |
subtype2 | 2 | 151 |
subtype3 | 1 | 297 |
P value = 0.753 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 367 | 87 |
subtype1 | 3 | 0 |
subtype2 | 121 | 32 |
subtype3 | 243 | 55 |
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Cluster data file = OV.mergedcluster.txt
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Clinical data file = OV.clin.merged.picked.txt
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Number of patients = 566
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Number of clustering approaches = 9
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Number of selected clinical features = 7
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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 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 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
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.