This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 14 different clustering approaches and 8 clinical features across 587 patients, 6 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 3 subtypes that do not correlate to any clinical features.
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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 3 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on array-based miR expression data identified 10 subtypes that correlate to 'AGE'.
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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 'AGE'.
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CNMF clustering analysis on RPPA data identified 3 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on RPPA data identified 4 subtypes that correlate to 'Time to Death'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'AGE'.
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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.
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3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes do not correlate to any clinical features.
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4 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes correlate to 'AGE'.
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2 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes do not correlate to any clinical features.
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3 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes do not correlate to any clinical features.
Clinical Features |
Time to Death |
AGE |
PRIMARY SITE OF DISEASE |
KARNOFSKY PERFORMANCE SCORE |
RADIATIONS RADIATION REGIMENINDICATION |
COMPLETENESS OF RESECTION |
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 |
0.0159 (1.00) |
0.00831 (0.773) |
0.432 (1.00) |
0.14 (1.00) |
0.795 (1.00) |
0.153 (1.00) |
0.0582 (1.00) |
0.152 (1.00) |
mRNA cHierClus subtypes |
0.253 (1.00) |
0.0223 (1.00) |
0.24 (1.00) |
0.407 (1.00) |
0.131 (1.00) |
0.154 (1.00) |
0.76 (1.00) |
0.0637 (1.00) |
miR CNMF subtypes |
0.0391 (1.00) |
0.691 (1.00) |
0.217 (1.00) |
0.669 (1.00) |
0.267 (1.00) |
0.212 (1.00) |
0.285 (1.00) |
0.232 (1.00) |
miR cHierClus subtypes |
0.106 (1.00) |
0.00044 (0.0423) |
0.802 (1.00) |
0.903 (1.00) |
0.36 (1.00) |
0.268 (1.00) |
0.908 (1.00) |
0.445 (1.00) |
Copy Number Ratio CNMF subtypes |
0.493 (1.00) |
1.4e-09 (1.38e-07) |
0.279 (1.00) |
0.769 (1.00) |
0.408 (1.00) |
0.272 (1.00) |
0.401 (1.00) |
0.367 (1.00) |
METHLYATION CNMF |
0.227 (1.00) |
4.02e-09 (3.94e-07) |
0.487 (1.00) |
0.728 (1.00) |
1 (1.00) |
0.481 (1.00) |
0.555 (1.00) |
0.553 (1.00) |
RPPA CNMF subtypes |
0.0245 (1.00) |
0.476 (1.00) |
0.769 (1.00) |
0.743 (1.00) |
0.133 (1.00) |
0.342 (1.00) |
0.886 (1.00) |
0.899 (1.00) |
RPPA cHierClus subtypes |
0.00165 (0.155) |
0.0367 (1.00) |
0.693 (1.00) |
0.253 (1.00) |
1 (1.00) |
0.879 (1.00) |
0.0754 (1.00) |
0.0924 (1.00) |
RNAseq CNMF subtypes |
0.416 (1.00) |
0.00134 (0.127) |
1 (1.00) |
1 (1.00) |
0.681 (1.00) |
0.469 (1.00) |
||
RNAseq cHierClus subtypes |
0.645 (1.00) |
0.0889 (1.00) |
0.554 (1.00) |
0.33 (1.00) |
0.265 (1.00) |
0.702 (1.00) |
0.778 (1.00) |
|
MIRSEQ CNMF |
0.301 (1.00) |
0.506 (1.00) |
0.0208 (1.00) |
0.235 (1.00) |
0.489 (1.00) |
0.552 (1.00) |
0.0478 (1.00) |
|
MIRSEQ CHIERARCHICAL |
0.28 (1.00) |
0.000116 (0.0113) |
0.87 (1.00) |
0.677 (1.00) |
0.685 (1.00) |
0.813 (1.00) |
0.77 (1.00) |
|
MIRseq Mature CNMF subtypes |
0.186 (1.00) |
0.434 (1.00) |
1 (1.00) |
0.0782 (1.00) |
||||
MIRseq Mature cHierClus subtypes |
0.0195 (1.00) |
0.308 (1.00) |
0.249 (1.00) |
1 (1.00) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 219 | 214 | 129 |
P value = 0.0159 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 557 | 293 | 0.3 - 180.2 (28.6) |
subtype1 | 216 | 124 | 0.3 - 152.0 (30.2) |
subtype2 | 212 | 93 | 0.4 - 180.2 (28.2) |
subtype3 | 129 | 76 | 0.3 - 119.1 (25.9) |
P value = 0.00831 (Kruskal-Wallis (anova)), Q value = 0.77
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 551 | 59.7 (11.6) |
subtype1 | 213 | 61.4 (11.6) |
subtype2 | 210 | 57.9 (11.4) |
subtype3 | 128 | 60.0 (11.7) |
P value = 0.432 (Fisher's exact test), Q value = 1
nPatients | OMENTUM | OVARY | PERITONEUM OVARY |
---|---|---|---|
ALL | 2 | 558 | 2 |
subtype1 | 0 | 219 | 0 |
subtype2 | 1 | 212 | 1 |
subtype3 | 1 | 127 | 1 |
P value = 0.14 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 75.6 (12.8) |
subtype1 | 31 | 78.1 (13.0) |
subtype2 | 28 | 76.4 (12.2) |
subtype3 | 19 | 70.5 (12.2) |
P value = 0.795 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 3 | 559 |
subtype1 | 2 | 217 |
subtype2 | 1 | 213 |
subtype3 | 0 | 129 |
P value = 0.153 (Fisher's exact test), Q value = 1
nPatients | R0 | R1 | R2 |
---|---|---|---|
ALL | 14 | 27 | 1 |
subtype1 | 6 | 9 | 0 |
subtype2 | 7 | 9 | 0 |
subtype3 | 1 | 9 | 1 |
P value = 0.0582 (Fisher's exact test), Q value = 1
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|---|
ALL | 2 | 19 | 24 | 1 | 485 |
subtype1 | 0 | 7 | 12 | 0 | 186 |
subtype2 | 0 | 11 | 9 | 1 | 181 |
subtype3 | 2 | 1 | 3 | 0 | 118 |
P value = 0.152 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 11 | 328 |
subtype1 | 6 | 130 |
subtype2 | 5 | 120 |
subtype3 | 0 | 78 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 313 | 160 | 89 |
P value = 0.253 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 557 | 293 | 0.3 - 180.2 (28.6) |
subtype1 | 309 | 155 | 0.3 - 130.0 (28.6) |
subtype2 | 160 | 87 | 0.3 - 180.2 (24.7) |
subtype3 | 88 | 51 | 1.0 - 152.0 (32.1) |
P value = 0.0223 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 551 | 59.7 (11.6) |
subtype1 | 307 | 59.5 (11.4) |
subtype2 | 157 | 58.4 (12.0) |
subtype3 | 87 | 62.9 (11.3) |
P value = 0.24 (Fisher's exact test), Q value = 1
nPatients | OMENTUM | OVARY | PERITONEUM OVARY |
---|---|---|---|
ALL | 2 | 558 | 2 |
subtype1 | 1 | 312 | 0 |
subtype2 | 1 | 157 | 2 |
subtype3 | 0 | 89 | 0 |
P value = 0.407 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 75.6 (12.8) |
subtype1 | 43 | 76.7 (11.5) |
subtype2 | 21 | 72.4 (13.4) |
subtype3 | 14 | 77.1 (15.4) |
P value = 0.131 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 3 | 559 |
subtype1 | 1 | 312 |
subtype2 | 0 | 160 |
subtype3 | 2 | 87 |
P value = 0.154 (Fisher's exact test), Q value = 1
nPatients | R0 | R1 | R2 |
---|---|---|---|
ALL | 14 | 27 | 1 |
subtype1 | 8 | 11 | 0 |
subtype2 | 2 | 12 | 1 |
subtype3 | 4 | 4 | 0 |
P value = 0.76 (Fisher's exact test), Q value = 1
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|---|
ALL | 2 | 19 | 24 | 1 | 485 |
subtype1 | 0 | 10 | 14 | 1 | 273 |
subtype2 | 2 | 6 | 6 | 0 | 136 |
subtype3 | 0 | 3 | 4 | 0 | 76 |
P value = 0.0637 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 11 | 328 |
subtype1 | 8 | 178 |
subtype2 | 0 | 93 |
subtype3 | 3 | 57 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 157 | 165 | 238 |
P value = 0.0391 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 555 | 293 | 0.3 - 180.2 (28.5) |
subtype1 | 156 | 88 | 0.3 - 130.0 (27.3) |
subtype2 | 162 | 92 | 0.3 - 115.9 (24.7) |
subtype3 | 237 | 113 | 0.3 - 180.2 (30.4) |
P value = 0.691 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 549 | 59.7 (11.6) |
subtype1 | 153 | 59.3 (12.5) |
subtype2 | 162 | 59.3 (11.6) |
subtype3 | 234 | 60.3 (11.1) |
P value = 0.217 (Fisher's exact test), Q value = 1
nPatients | OMENTUM | OVARY | PERITONEUM OVARY |
---|---|---|---|
ALL | 2 | 556 | 2 |
subtype1 | 0 | 155 | 2 |
subtype2 | 1 | 164 | 0 |
subtype3 | 1 | 237 | 0 |
P value = 0.669 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 75.6 (12.8) |
subtype1 | 24 | 76.7 (12.7) |
subtype2 | 23 | 73.9 (15.3) |
subtype3 | 31 | 76.1 (10.9) |
P value = 0.267 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 3 | 557 |
subtype1 | 0 | 157 |
subtype2 | 0 | 165 |
subtype3 | 3 | 235 |
P value = 0.212 (Fisher's exact test), Q value = 1
nPatients | R0 | R1 | R2 |
---|---|---|---|
ALL | 14 | 27 | 1 |
subtype1 | 4 | 12 | 0 |
subtype2 | 3 | 9 | 1 |
subtype3 | 7 | 6 | 0 |
P value = 0.285 (Fisher's exact test), Q value = 1
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|---|
ALL | 2 | 19 | 23 | 1 | 484 |
subtype1 | 0 | 2 | 8 | 0 | 136 |
subtype2 | 2 | 6 | 5 | 0 | 143 |
subtype3 | 0 | 11 | 10 | 1 | 205 |
P value = 0.232 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 11 | 327 |
subtype1 | 5 | 86 |
subtype2 | 1 | 97 |
subtype3 | 5 | 144 |
Cluster Labels | 1 | 10 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |
---|---|---|---|---|---|---|---|---|---|---|
Number of samples | 82 | 57 | 58 | 86 | 35 | 75 | 36 | 36 | 51 | 44 |
P value = 0.106 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 555 | 293 | 0.3 - 180.2 (28.5) |
subtype1 | 82 | 46 | 0.3 - 130.0 (25.4) |
subtype10 | 56 | 28 | 0.8 - 115.9 (25.6) |
subtype2 | 56 | 35 | 0.3 - 106.0 (26.0) |
subtype3 | 86 | 42 | 0.3 - 125.8 (30.6) |
subtype4 | 35 | 25 | 1.2 - 101.8 (22.2) |
subtype5 | 74 | 36 | 1.7 - 180.2 (34.3) |
subtype6 | 36 | 19 | 1.0 - 73.5 (32.0) |
subtype7 | 36 | 13 | 0.5 - 98.0 (30.0) |
subtype8 | 50 | 25 | 0.5 - 152.0 (21.6) |
subtype9 | 44 | 24 | 1.0 - 107.2 (29.7) |
P value = 0.00044 (Kruskal-Wallis (anova)), Q value = 0.042
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 549 | 59.7 (11.6) |
subtype1 | 79 | 58.6 (12.2) |
subtype10 | 56 | 55.6 (11.2) |
subtype2 | 58 | 61.7 (12.3) |
subtype3 | 85 | 59.3 (11.2) |
subtype4 | 35 | 60.3 (11.7) |
subtype5 | 74 | 60.0 (10.0) |
subtype6 | 35 | 63.3 (10.9) |
subtype7 | 35 | 62.9 (12.0) |
subtype8 | 49 | 63.6 (11.4) |
subtype9 | 43 | 54.3 (11.3) |
P value = 0.802 (Fisher's exact test), Q value = 1
nPatients | OMENTUM | OVARY | PERITONEUM OVARY |
---|---|---|---|
ALL | 2 | 556 | 2 |
subtype1 | 0 | 81 | 1 |
subtype10 | 0 | 57 | 0 |
subtype2 | 0 | 58 | 0 |
subtype3 | 1 | 85 | 0 |
subtype4 | 0 | 34 | 1 |
subtype5 | 1 | 74 | 0 |
subtype6 | 0 | 36 | 0 |
subtype7 | 0 | 36 | 0 |
subtype8 | 0 | 51 | 0 |
subtype9 | 0 | 44 | 0 |
P value = 0.903 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 75.6 (12.8) |
subtype1 | 13 | 73.8 (15.0) |
subtype10 | 6 | 73.3 (16.3) |
subtype2 | 4 | 75.0 (10.0) |
subtype3 | 13 | 80.0 (11.5) |
subtype4 | 3 | 73.3 (11.5) |
subtype5 | 12 | 76.7 (16.7) |
subtype6 | 7 | 77.1 (13.8) |
subtype7 | 6 | 76.7 (8.2) |
subtype8 | 5 | 68.0 (11.0) |
subtype9 | 9 | 75.6 (8.8) |
P value = 0.36 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 3 | 557 |
subtype1 | 0 | 82 |
subtype10 | 0 | 57 |
subtype2 | 0 | 58 |
subtype3 | 0 | 86 |
subtype4 | 0 | 35 |
subtype5 | 1 | 74 |
subtype6 | 0 | 36 |
subtype7 | 1 | 35 |
subtype8 | 1 | 50 |
subtype9 | 0 | 44 |
P value = 0.268 (Fisher's exact test), Q value = 1
nPatients | R0 | R1 | R2 |
---|---|---|---|
ALL | 14 | 27 | 1 |
subtype1 | 2 | 7 | 0 |
subtype10 | 2 | 1 | 0 |
subtype2 | 1 | 2 | 0 |
subtype3 | 2 | 4 | 0 |
subtype4 | 0 | 5 | 0 |
subtype5 | 1 | 6 | 0 |
subtype6 | 1 | 1 | 0 |
subtype7 | 2 | 1 | 0 |
subtype8 | 2 | 0 | 0 |
subtype9 | 1 | 0 | 1 |
P value = 0.908 (Fisher's exact test), Q value = 1
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|---|
ALL | 2 | 19 | 23 | 1 | 484 |
subtype1 | 0 | 1 | 3 | 0 | 71 |
subtype10 | 1 | 2 | 4 | 0 | 47 |
subtype2 | 0 | 2 | 5 | 0 | 47 |
subtype3 | 0 | 4 | 4 | 1 | 73 |
subtype4 | 0 | 0 | 1 | 0 | 33 |
subtype5 | 1 | 3 | 2 | 0 | 66 |
subtype6 | 0 | 1 | 0 | 0 | 34 |
subtype7 | 0 | 1 | 1 | 0 | 32 |
subtype8 | 0 | 4 | 1 | 0 | 42 |
subtype9 | 0 | 1 | 2 | 0 | 39 |
P value = 0.445 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 11 | 327 |
subtype1 | 3 | 45 |
subtype10 | 0 | 36 |
subtype2 | 0 | 24 |
subtype3 | 3 | 56 |
subtype4 | 1 | 18 |
subtype5 | 1 | 44 |
subtype6 | 2 | 23 |
subtype7 | 1 | 19 |
subtype8 | 0 | 34 |
subtype9 | 0 | 28 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 170 | 201 | 200 |
P value = 0.493 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 556 | 290 | 0.3 - 180.2 (28.0) |
subtype1 | 165 | 94 | 0.8 - 119.1 (29.4) |
subtype2 | 196 | 95 | 0.3 - 130.0 (30.0) |
subtype3 | 195 | 101 | 0.3 - 180.2 (22.5) |
P value = 1.4e-09 (Kruskal-Wallis (anova)), Q value = 1.4e-07
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 550 | 59.8 (11.6) |
subtype1 | 163 | 60.2 (12.2) |
subtype2 | 197 | 56.1 (10.9) |
subtype3 | 190 | 63.3 (10.6) |
P value = 0.279 (Fisher's exact test), Q value = 1
nPatients | OMENTUM | OVARY | PERITONEUM OVARY |
---|---|---|---|
ALL | 2 | 557 | 2 |
subtype1 | 1 | 166 | 0 |
subtype2 | 0 | 198 | 0 |
subtype3 | 1 | 193 | 2 |
P value = 0.769 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 81 | 75.4 (13.7) |
subtype1 | 22 | 77.3 (11.2) |
subtype2 | 31 | 74.8 (12.9) |
subtype3 | 28 | 74.6 (16.4) |
P value = 0.408 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 3 | 568 |
subtype1 | 1 | 169 |
subtype2 | 0 | 201 |
subtype3 | 2 | 198 |
P value = 0.272 (Fisher's exact test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 14 | 26 | 5 | 3 |
subtype1 | 2 | 11 | 0 | 1 |
subtype2 | 3 | 6 | 2 | 1 |
subtype3 | 9 | 9 | 3 | 1 |
P value = 0.401 (Fisher's exact test), Q value = 1
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|---|
ALL | 3 | 18 | 32 | 1 | 475 |
subtype1 | 1 | 3 | 7 | 0 | 145 |
subtype2 | 0 | 9 | 15 | 1 | 163 |
subtype3 | 2 | 6 | 10 | 0 | 167 |
P value = 0.367 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 10 | 325 |
subtype1 | 1 | 101 |
subtype2 | 4 | 111 |
subtype3 | 5 | 113 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 175 | 180 | 219 |
P value = 0.227 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 558 | 295 | 0.3 - 180.2 (28.5) |
subtype1 | 170 | 101 | 0.3 - 152.0 (26.9) |
subtype2 | 172 | 86 | 0.8 - 180.2 (30.1) |
subtype3 | 216 | 108 | 0.3 - 130.0 (28.4) |
P value = 4.02e-09 (Kruskal-Wallis (anova)), Q value = 3.9e-07
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 553 | 59.8 (11.6) |
subtype1 | 168 | 64.5 (10.4) |
subtype2 | 170 | 57.8 (12.3) |
subtype3 | 215 | 57.7 (10.9) |
P value = 0.487 (Fisher's exact test), Q value = 1
nPatients | OMENTUM | OVARY | PERITONEUM OVARY |
---|---|---|---|
ALL | 2 | 560 | 2 |
subtype1 | 0 | 170 | 1 |
subtype2 | 0 | 175 | 0 |
subtype3 | 2 | 215 | 1 |
P value = 0.728 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 75.6 (12.8) |
subtype1 | 22 | 74.5 (12.6) |
subtype2 | 21 | 75.2 (14.0) |
subtype3 | 35 | 76.6 (12.4) |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 3 | 571 |
subtype1 | 1 | 174 |
subtype2 | 1 | 179 |
subtype3 | 1 | 218 |
P value = 0.481 (Fisher's exact test), Q value = 1
nPatients | R0 | R1 | R2 |
---|---|---|---|
ALL | 14 | 26 | 2 |
subtype1 | 4 | 8 | 1 |
subtype2 | 4 | 12 | 0 |
subtype3 | 6 | 6 | 1 |
P value = 0.555 (Fisher's exact test), Q value = 1
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|---|
ALL | 3 | 18 | 24 | 1 | 486 |
subtype1 | 1 | 3 | 9 | 0 | 151 |
subtype2 | 1 | 8 | 4 | 0 | 151 |
subtype3 | 1 | 7 | 11 | 1 | 184 |
P value = 0.553 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 11 | 329 |
subtype1 | 5 | 102 |
subtype2 | 2 | 104 |
subtype3 | 4 | 123 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 123 | 199 | 85 |
P value = 0.0245 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 401 | 213 | 0.3 - 180.2 (28.7) |
subtype1 | 120 | 66 | 0.4 - 125.8 (31.1) |
subtype2 | 197 | 92 | 0.3 - 180.2 (25.1) |
subtype3 | 84 | 55 | 0.5 - 89.3 (27.2) |
P value = 0.476 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 400 | 59.7 (11.8) |
subtype1 | 121 | 60.0 (12.4) |
subtype2 | 196 | 59.2 (11.7) |
subtype3 | 83 | 60.4 (11.4) |
P value = 0.769 (Fisher's exact test), Q value = 1
nPatients | OMENTUM | OVARY | PERITONEUM OVARY |
---|---|---|---|
ALL | 2 | 403 | 2 |
subtype1 | 1 | 122 | 0 |
subtype2 | 1 | 197 | 1 |
subtype3 | 0 | 84 | 1 |
P value = 0.743 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 51 | 74.9 (11.9) |
subtype1 | 21 | 76.2 (10.2) |
subtype2 | 24 | 75.0 (12.2) |
subtype3 | 6 | 70.0 (16.7) |
P value = 0.133 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 2 | 405 |
subtype1 | 2 | 121 |
subtype2 | 0 | 199 |
subtype3 | 0 | 85 |
P value = 0.342 (Fisher's exact test), Q value = 1
nPatients | R0 | R1 | R2 |
---|---|---|---|
ALL | 13 | 28 | 2 |
subtype1 | 2 | 10 | 0 |
subtype2 | 8 | 9 | 1 |
subtype3 | 3 | 9 | 1 |
P value = 0.886 (Fisher's exact test), Q value = 1
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 3 | 16 | 19 | 342 |
subtype1 | 2 | 5 | 6 | 100 |
subtype2 | 1 | 9 | 10 | 169 |
subtype3 | 0 | 2 | 3 | 73 |
P value = 0.899 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 207 |
subtype1 | 2 | 65 |
subtype2 | 5 | 102 |
subtype3 | 1 | 40 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 120 | 98 | 130 | 59 |
P value = 0.00165 (logrank test), Q value = 0.16
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 401 | 213 | 0.3 - 180.2 (28.7) |
subtype1 | 119 | 77 | 0.4 - 125.8 (25.9) |
subtype2 | 95 | 43 | 0.3 - 115.9 (28.4) |
subtype3 | 128 | 59 | 0.5 - 152.0 (26.4) |
subtype4 | 59 | 34 | 0.8 - 180.2 (36.2) |
P value = 0.0367 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 400 | 59.7 (11.8) |
subtype1 | 119 | 60.7 (12.0) |
subtype2 | 96 | 58.3 (12.7) |
subtype3 | 127 | 58.5 (11.1) |
subtype4 | 58 | 62.5 (11.2) |
P value = 0.693 (Fisher's exact test), Q value = 1
nPatients | OMENTUM | OVARY | PERITONEUM OVARY |
---|---|---|---|
ALL | 2 | 403 | 2 |
subtype1 | 1 | 118 | 1 |
subtype2 | 0 | 98 | 0 |
subtype3 | 0 | 129 | 1 |
subtype4 | 1 | 58 | 0 |
P value = 0.253 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 51 | 74.9 (11.9) |
subtype1 | 9 | 75.6 (8.8) |
subtype2 | 6 | 83.3 (8.2) |
subtype3 | 28 | 74.3 (12.0) |
subtype4 | 8 | 70.0 (15.1) |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 2 | 405 |
subtype1 | 1 | 119 |
subtype2 | 0 | 98 |
subtype3 | 1 | 129 |
subtype4 | 0 | 59 |
P value = 0.879 (Fisher's exact test), Q value = 1
nPatients | R0 | R1 | R2 |
---|---|---|---|
ALL | 13 | 28 | 2 |
subtype1 | 3 | 11 | 1 |
subtype2 | 4 | 4 | 0 |
subtype3 | 5 | 10 | 1 |
subtype4 | 1 | 3 | 0 |
P value = 0.0754 (Fisher's exact test), Q value = 1
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 3 | 16 | 19 | 342 |
subtype1 | 1 | 2 | 5 | 105 |
subtype2 | 0 | 4 | 1 | 85 |
subtype3 | 2 | 9 | 7 | 103 |
subtype4 | 0 | 1 | 6 | 49 |
P value = 0.0924 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 207 |
subtype1 | 0 | 64 |
subtype2 | 1 | 44 |
subtype3 | 5 | 75 |
subtype4 | 2 | 24 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 102 | 67 | 92 |
P value = 0.416 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 259 | 147 | 0.3 - 180.2 (28.2) |
subtype1 | 102 | 55 | 0.4 - 180.2 (28.5) |
subtype2 | 66 | 36 | 1.0 - 106.0 (34.6) |
subtype3 | 91 | 56 | 0.3 - 152.0 (25.0) |
P value = 0.00134 (Kruskal-Wallis (anova)), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 254 | 59.0 (10.8) |
subtype1 | 99 | 59.2 (10.3) |
subtype2 | 66 | 55.2 (10.6) |
subtype3 | 89 | 61.5 (10.9) |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | OMENTUM | OVARY |
---|---|---|
ALL | 1 | 260 |
subtype1 | 1 | 101 |
subtype2 | 0 | 67 |
subtype3 | 0 | 92 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 2 | 259 |
subtype1 | 1 | 101 |
subtype2 | 0 | 67 |
subtype3 | 1 | 91 |
P value = 0.681 (Fisher's exact test), Q value = 1
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|---|
ALL | 1 | 12 | 16 | 1 | 222 |
subtype1 | 1 | 6 | 5 | 0 | 86 |
subtype2 | 0 | 3 | 3 | 1 | 58 |
subtype3 | 0 | 3 | 8 | 0 | 78 |
P value = 0.469 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 3 | 137 |
subtype1 | 2 | 53 |
subtype2 | 1 | 34 |
subtype3 | 0 | 50 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 107 | 117 | 37 |
P value = 0.645 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 259 | 147 | 0.3 - 180.2 (28.2) |
subtype1 | 106 | 55 | 0.4 - 180.2 (27.7) |
subtype2 | 116 | 68 | 0.3 - 125.8 (30.3) |
subtype3 | 37 | 24 | 1.0 - 152.0 (25.7) |
P value = 0.0889 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 254 | 59.0 (10.8) |
subtype1 | 105 | 59.0 (10.6) |
subtype2 | 113 | 57.6 (10.5) |
subtype3 | 36 | 62.9 (11.9) |
P value = 0.554 (Fisher's exact test), Q value = 1
nPatients | OMENTUM | OVARY |
---|---|---|
ALL | 1 | 260 |
subtype1 | 1 | 106 |
subtype2 | 0 | 117 |
subtype3 | 0 | 37 |
P value = 0.33 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 14 | 74.3 (12.2) |
subtype1 | 11 | 72.7 (13.5) |
subtype2 | 3 | 80.0 (0.0) |
P value = 0.265 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 2 | 259 |
subtype1 | 0 | 107 |
subtype2 | 1 | 116 |
subtype3 | 1 | 36 |
P value = 0.702 (Fisher's exact test), Q value = 1
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|---|
ALL | 1 | 12 | 16 | 1 | 222 |
subtype1 | 1 | 6 | 5 | 0 | 90 |
subtype2 | 0 | 4 | 7 | 1 | 102 |
subtype3 | 0 | 2 | 4 | 0 | 30 |
P value = 0.778 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 3 | 137 |
subtype1 | 2 | 54 |
subtype2 | 1 | 59 |
subtype3 | 0 | 24 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 124 | 185 | 144 |
P value = 0.301 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 450 | 252 | 0.3 - 180.2 (30.1) |
subtype1 | 124 | 78 | 0.3 - 152.0 (28.6) |
subtype2 | 184 | 98 | 0.3 - 180.2 (32.1) |
subtype3 | 142 | 76 | 0.3 - 130.0 (28.7) |
P value = 0.506 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 445 | 59.8 (11.5) |
subtype1 | 123 | 60.7 (11.7) |
subtype2 | 182 | 59.4 (11.3) |
subtype3 | 140 | 59.4 (11.6) |
P value = 0.0208 (Fisher's exact test), Q value = 1
nPatients | OMENTUM | OVARY | PERITONEUM OVARY |
---|---|---|---|
ALL | 2 | 450 | 1 |
subtype1 | 2 | 121 | 1 |
subtype2 | 0 | 185 | 0 |
subtype3 | 0 | 144 | 0 |
P value = 0.235 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 64 | 75.3 (13.2) |
subtype1 | 11 | 81.8 (14.0) |
subtype2 | 45 | 74.2 (12.5) |
subtype3 | 8 | 72.5 (14.9) |
P value = 0.489 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 3 | 450 |
subtype1 | 0 | 124 |
subtype2 | 1 | 184 |
subtype3 | 2 | 142 |
P value = 0.552 (Fisher's exact test), Q value = 1
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 15 | 21 | 400 |
subtype1 | 2 | 3 | 6 | 106 |
subtype2 | 0 | 6 | 10 | 166 |
subtype3 | 0 | 6 | 5 | 128 |
P value = 0.0478 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 262 |
subtype1 | 0 | 66 |
subtype2 | 7 | 113 |
subtype3 | 1 | 83 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 105 | 73 | 169 | 106 |
P value = 0.28 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 450 | 252 | 0.3 - 180.2 (30.1) |
subtype1 | 105 | 53 | 0.3 - 107.2 (32.8) |
subtype2 | 72 | 45 | 1.0 - 89.3 (28.0) |
subtype3 | 168 | 99 | 0.3 - 180.2 (28.3) |
subtype4 | 105 | 55 | 0.3 - 130.0 (30.5) |
P value = 0.000116 (Kruskal-Wallis (anova)), Q value = 0.011
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 445 | 59.8 (11.5) |
subtype1 | 104 | 56.9 (11.5) |
subtype2 | 73 | 62.5 (11.8) |
subtype3 | 166 | 61.8 (11.1) |
subtype4 | 102 | 57.4 (10.9) |
P value = 0.87 (Fisher's exact test), Q value = 1
nPatients | OMENTUM | OVARY | PERITONEUM OVARY |
---|---|---|---|
ALL | 2 | 450 | 1 |
subtype1 | 0 | 105 | 0 |
subtype2 | 0 | 73 | 0 |
subtype3 | 2 | 166 | 1 |
subtype4 | 0 | 106 | 0 |
P value = 0.677 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 64 | 75.3 (13.2) |
subtype1 | 28 | 76.4 (11.0) |
subtype2 | 6 | 70.0 (21.0) |
subtype3 | 26 | 74.6 (14.5) |
subtype4 | 4 | 80.0 (0.0) |
P value = 0.685 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 3 | 450 |
subtype1 | 0 | 105 |
subtype2 | 1 | 72 |
subtype3 | 1 | 168 |
subtype4 | 1 | 105 |
P value = 0.813 (Fisher's exact test), Q value = 1
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 15 | 21 | 400 |
subtype1 | 0 | 6 | 4 | 94 |
subtype2 | 0 | 3 | 4 | 61 |
subtype3 | 1 | 3 | 8 | 151 |
subtype4 | 1 | 3 | 5 | 94 |
P value = 0.77 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 262 |
subtype1 | 3 | 70 |
subtype2 | 2 | 45 |
subtype3 | 2 | 90 |
subtype4 | 1 | 57 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 12 | 10 |
P value = 0.186 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 22 | 14 | 0.8 - 125.8 (30.4) |
subtype1 | 12 | 8 | 0.8 - 125.8 (22.9) |
subtype2 | 10 | 6 | 5.4 - 115.9 (59.9) |
P value = 0.434 (Wilcoxon-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 21 | 60.5 (12.6) |
subtype1 | 12 | 62.6 (13.1) |
subtype2 | 9 | 57.7 (12.1) |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | OMENTUM | OVARY |
---|---|---|
ALL | 1 | 21 |
subtype1 | 1 | 11 |
subtype2 | 0 | 10 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 6 | 2 | 2 | 6 | 4 | 2 |
P value = 0.0195 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 16 | 10 | 4.8 - 125.8 (34.0) |
subtype1 | 6 | 5 | 4.8 - 42.0 (24.9) |
subtype4 | 6 | 2 | 5.4 - 115.9 (59.9) |
subtype5 | 4 | 3 | 11.1 - 125.8 (51.8) |
P value = 0.308 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 15 | 57.6 (12.9) |
subtype1 | 6 | 54.3 (17.4) |
subtype4 | 5 | 55.2 (7.7) |
subtype5 | 4 | 65.5 (9.1) |
P value = 0.249 (Fisher's exact test), Q value = 1
nPatients | OMENTUM | OVARY |
---|---|---|
ALL | 1 | 15 |
subtype1 | 0 | 6 |
subtype4 | 0 | 6 |
subtype5 | 1 | 3 |
-
Cluster data file = OV-TP.mergedcluster.txt
-
Clinical data file = OV-TP.merged_data.txt
-
Number of patients = 587
-
Number of clustering approaches = 14
-
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.