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 7 clinical features across 589 patients, 16 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 'Time to Death' and 'YEARS_TO_BIRTH'.
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Consensus hierarchical clustering analysis on array-based mRNA expression data identified 3 subtypes that correlate to 'YEARS_TO_BIRTH'.
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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 10 subtypes that correlate to 'YEARS_TO_BIRTH'.
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3 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes correlate to 'YEARS_TO_BIRTH'.
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4 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'YEARS_TO_BIRTH' and 'RADIATION_THERAPY'.
-
CNMF clustering analysis on RPPA data identified 3 subtypes that correlate to 'Time to Death'.
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Consensus hierarchical clustering analysis on RPPA data identified 4 subtypes that correlate to 'Time to Death' and 'YEARS_TO_BIRTH'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'YEARS_TO_BIRTH' and 'ETHNICITY'.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'YEARS_TO_BIRTH'.
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4 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'Time to Death'.
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4 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes correlate to 'YEARS_TO_BIRTH'.
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4 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes do not correlate to any clinical features.
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4 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 |
YEARS TO BIRTH |
TUMOR TISSUE SITE |
RADIATION THERAPY |
KARNOFSKY PERFORMANCE SCORE |
RESIDUAL TUMOR |
ETHNICITY |
Statistical Tests | logrank test | Kruskal-Wallis (anova) | Fisher's exact test | Fisher's exact test | Kruskal-Wallis (anova) | Fisher's exact test | Fisher's exact test |
mRNA CNMF subtypes |
0.0362 (0.232) |
0.0104 (0.127) |
0.388 (0.835) |
1 (1.00) |
0.385 (0.835) |
0.258 (0.703) |
0.315 (0.779) |
mRNA cHierClus subtypes |
0.147 (0.539) |
0.0233 (0.19) |
0.242 (0.698) |
1 (1.00) |
0.407 (0.84) |
0.154 (0.539) |
0.0635 (0.328) |
miR CNMF subtypes |
0.00157 (0.0257) |
0.965 (1.00) |
0.12 (0.539) |
0.855 (1.00) |
0.735 (1.00) |
0.322 (0.779) |
0.456 (0.844) |
miR cHierClus subtypes |
0.188 (0.613) |
0.000445 (0.0109) |
0.804 (1.00) |
0.249 (0.698) |
0.903 (1.00) |
0.266 (0.705) |
0.437 (0.84) |
Copy Number Ratio CNMF subtypes |
0.69 (1.00) |
1.16e-09 (5.71e-08) |
0.392 (0.835) |
0.135 (0.539) |
0.334 (0.78) |
0.485 (0.849) |
0.774 (1.00) |
METHLYATION CNMF |
0.139 (0.539) |
4.84e-12 (4.75e-10) |
0.411 (0.84) |
0.012 (0.13) |
0.246 (0.698) |
0.852 (1.00) |
0.654 (1.00) |
RPPA CNMF subtypes |
0.0268 (0.202) |
0.453 (0.844) |
1 (1.00) |
0.532 (0.869) |
0.481 (0.849) |
0.314 (0.779) |
0.723 (1.00) |
RPPA cHierClus subtypes |
0.00323 (0.0452) |
0.0379 (0.232) |
0.0526 (0.303) |
0.904 (1.00) |
0.938 (1.00) |
0.518 (0.86) |
0.117 (0.539) |
RNAseq CNMF subtypes |
0.791 (1.00) |
0.000846 (0.0166) |
0.784 (1.00) |
0.199 (0.625) |
0.427 (0.84) |
0.51 (0.86) |
0.0183 (0.163) |
RNAseq cHierClus subtypes |
0.124 (0.539) |
0.0145 (0.142) |
0.59 (0.932) |
0.467 (0.847) |
0.204 (0.625) |
0.589 (0.932) |
0.326 (0.779) |
MIRSEQ CNMF |
0.0353 (0.232) |
0.911 (1.00) |
0.0579 (0.315) |
1 (1.00) |
0.98 (1.00) |
0.631 (0.982) |
|
MIRSEQ CHIERARCHICAL |
0.15 (0.539) |
0.000116 (0.00379) |
0.869 (1.00) |
0.514 (0.86) |
0.677 (1.00) |
0.773 (1.00) |
|
MIRseq Mature CNMF subtypes |
0.183 (0.613) |
0.374 (0.835) |
1 (1.00) |
||||
MIRseq Mature cHierClus subtypes |
0.136 (0.539) |
0.434 (0.84) |
1 (1.00) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 181 | 113 | 120 | 149 |
P value = 0.0362 (logrank test), Q value = 0.23
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 559 | 334 | 0.3 - 180.2 (33.1) |
subtype1 | 180 | 108 | 0.3 - 152.0 (33.1) |
subtype2 | 113 | 77 | 0.3 - 153.4 (31.0) |
subtype3 | 120 | 83 | 1.2 - 123.2 (37.8) |
subtype4 | 146 | 66 | 0.4 - 180.2 (32.2) |
P value = 0.0104 (Kruskal-Wallis (anova)), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.7 (11.6) |
subtype1 | 175 | 61.9 (11.7) |
subtype2 | 112 | 60.3 (11.9) |
subtype3 | 119 | 58.3 (11.1) |
subtype4 | 146 | 57.9 (11.4) |
P value = 0.388 (Fisher's exact test), Q value = 0.84
nPatients | OMENTUM | OVARY | PERITONEUM OVARY |
---|---|---|---|
ALL | 2 | 559 | 2 |
subtype1 | 0 | 181 | 0 |
subtype2 | 1 | 111 | 1 |
subtype3 | 0 | 120 | 0 |
subtype4 | 1 | 147 | 1 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 541 | 5 |
subtype1 | 173 | 2 |
subtype2 | 108 | 1 |
subtype3 | 118 | 1 |
subtype4 | 142 | 1 |
P value = 0.385 (Kruskal-Wallis (anova)), Q value = 0.84
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 75.6 (12.8) |
subtype1 | 21 | 75.2 (14.0) |
subtype2 | 16 | 71.2 (12.6) |
subtype3 | 24 | 76.7 (12.7) |
subtype4 | 17 | 78.8 (11.1) |
P value = 0.258 (Fisher's exact test), Q value = 0.7
nPatients | R0 | R1 | R2 |
---|---|---|---|
ALL | 14 | 27 | 1 |
subtype1 | 7 | 7 | 0 |
subtype2 | 1 | 8 | 1 |
subtype3 | 1 | 3 | 0 |
subtype4 | 5 | 9 | 0 |
P value = 0.315 (Fisher's exact test), Q value = 0.78
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 11 | 330 |
subtype1 | 5 | 109 |
subtype2 | 0 | 69 |
subtype3 | 2 | 73 |
subtype4 | 4 | 79 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 313 | 161 | 89 |
P value = 0.147 (logrank test), Q value = 0.54
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 559 | 334 | 0.3 - 180.2 (33.1) |
subtype1 | 309 | 174 | 0.3 - 153.4 (33.9) |
subtype2 | 161 | 101 | 0.3 - 180.2 (30.1) |
subtype3 | 89 | 59 | 0.8 - 152.0 (38.4) |
P value = 0.0233 (Kruskal-Wallis (anova)), Q value = 0.19
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.7 (11.6) |
subtype1 | 307 | 59.5 (11.4) |
subtype2 | 158 | 58.4 (12.0) |
subtype3 | 87 | 62.9 (11.3) |
P value = 0.242 (Fisher's exact test), Q value = 0.7
nPatients | OMENTUM | OVARY | PERITONEUM OVARY |
---|---|---|---|
ALL | 2 | 559 | 2 |
subtype1 | 1 | 312 | 0 |
subtype2 | 1 | 158 | 2 |
subtype3 | 0 | 89 | 0 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 541 | 5 |
subtype1 | 301 | 3 |
subtype2 | 154 | 1 |
subtype3 | 86 | 1 |
P value = 0.407 (Kruskal-Wallis (anova)), Q value = 0.84
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 = 0.154 (Fisher's exact test), Q value = 0.54
nPatients | R0 | R1 | R2 |
---|---|---|---|
ALL | 14 | 27 | 1 |
subtype1 | 8 | 11 | 0 |
subtype2 | 2 | 12 | 1 |
subtype3 | 4 | 4 | 0 |
P value = 0.0635 (Fisher's exact test), Q value = 0.33
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 11 | 330 |
subtype1 | 8 | 179 |
subtype2 | 0 | 94 |
subtype3 | 3 | 57 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 181 | 133 | 247 |
P value = 0.00157 (logrank test), Q value = 0.026
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 557 | 334 | 0.3 - 180.2 (33.1) |
subtype1 | 181 | 111 | 0.3 - 153.4 (32.1) |
subtype2 | 129 | 85 | 0.3 - 145.4 (29.1) |
subtype3 | 247 | 138 | 0.3 - 180.2 (36.3) |
P value = 0.965 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 550 | 59.7 (11.6) |
subtype1 | 177 | 59.6 (12.3) |
subtype2 | 131 | 59.4 (11.6) |
subtype3 | 242 | 60.0 (11.1) |
P value = 0.12 (Fisher's exact test), Q value = 0.54
nPatients | OMENTUM | OVARY | PERITONEUM OVARY |
---|---|---|---|
ALL | 2 | 557 | 2 |
subtype1 | 1 | 178 | 2 |
subtype2 | 1 | 132 | 0 |
subtype3 | 0 | 247 | 0 |
P value = 0.855 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 539 | 5 |
subtype1 | 173 | 1 |
subtype2 | 127 | 1 |
subtype3 | 239 | 3 |
P value = 0.735 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 75.6 (12.8) |
subtype1 | 25 | 76.8 (12.5) |
subtype2 | 17 | 74.1 (15.4) |
subtype3 | 36 | 75.6 (11.8) |
P value = 0.322 (Fisher's exact test), Q value = 0.78
nPatients | R0 | R1 | R2 |
---|---|---|---|
ALL | 14 | 27 | 1 |
subtype1 | 5 | 12 | 0 |
subtype2 | 2 | 7 | 1 |
subtype3 | 7 | 8 | 0 |
P value = 0.456 (Fisher's exact test), Q value = 0.84
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 11 | 329 |
subtype1 | 5 | 101 |
subtype2 | 1 | 79 |
subtype3 | 5 | 149 |
Cluster Labels | 1 | 10 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |
---|---|---|---|---|---|---|---|---|---|---|
Number of samples | 83 | 57 | 58 | 86 | 35 | 75 | 36 | 36 | 51 | 44 |
P value = 0.188 (logrank test), Q value = 0.61
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 557 | 334 | 0.3 - 180.2 (33.1) |
subtype1 | 83 | 52 | 0.3 - 153.4 (31.2) |
subtype10 | 56 | 30 | 2.0 - 115.9 (28.2) |
subtype2 | 58 | 37 | 0.3 - 106.0 (28.3) |
subtype3 | 86 | 48 | 0.3 - 127.3 (36.8) |
subtype4 | 34 | 26 | 1.2 - 134.0 (33.6) |
subtype5 | 74 | 43 | 1.7 - 180.2 (38.6) |
subtype6 | 36 | 25 | 1.0 - 125.6 (35.8) |
subtype7 | 36 | 16 | 6.1 - 124.4 (31.7) |
subtype8 | 50 | 28 | 0.5 - 152.0 (26.7) |
subtype9 | 44 | 29 | 1.0 - 127.8 (32.2) |
P value = 0.000445 (Kruskal-Wallis (anova)), Q value = 0.011
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 550 | 59.7 (11.6) |
subtype1 | 80 | 58.7 (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 = 0.804 (Fisher's exact test), Q value = 1
nPatients | OMENTUM | OVARY | PERITONEUM OVARY |
---|---|---|---|
ALL | 2 | 557 | 2 |
subtype1 | 0 | 82 | 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 = 0.249 (Fisher's exact test), Q value = 0.7
nPatients | NO | YES |
---|---|---|
ALL | 539 | 5 |
subtype1 | 77 | 1 |
subtype10 | 55 | 0 |
subtype2 | 56 | 1 |
subtype3 | 85 | 0 |
subtype4 | 34 | 0 |
subtype5 | 74 | 0 |
subtype6 | 35 | 0 |
subtype7 | 33 | 1 |
subtype8 | 48 | 2 |
subtype9 | 42 | 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 = 0.266 (Fisher's exact test), Q value = 0.7
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 = 0.437 (Fisher's exact test), Q value = 0.84
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 11 | 329 |
subtype1 | 3 | 46 |
subtype10 | 0 | 36 |
subtype2 | 0 | 25 |
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 | 241 | 129 | 203 |
P value = 0.69 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 559 | 331 | 0.3 - 180.2 (32.9) |
subtype1 | 235 | 138 | 0.3 - 180.2 (29.1) |
subtype2 | 126 | 80 | 0.8 - 153.4 (33.6) |
subtype3 | 198 | 113 | 0.3 - 134.0 (34.9) |
P value = 1.16e-09 (Kruskal-Wallis (anova)), Q value = 5.7e-08
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
subtype1 | 231 | 63.4 (10.7) |
subtype2 | 123 | 58.6 (12.5) |
subtype3 | 198 | 56.5 (10.8) |
P value = 0.392 (Fisher's exact test), Q value = 0.84
nPatients | OMENTUM | OVARY | PERITONEUM OVARY |
---|---|---|---|
ALL | 3 | 558 | 2 |
subtype1 | 2 | 233 | 2 |
subtype2 | 1 | 126 | 0 |
subtype3 | 0 | 199 | 0 |
P value = 0.135 (Fisher's exact test), Q value = 0.54
nPatients | NO | YES |
---|---|---|
ALL | 541 | 5 |
subtype1 | 229 | 1 |
subtype2 | 118 | 3 |
subtype3 | 194 | 1 |
P value = 0.334 (Kruskal-Wallis (anova)), Q value = 0.78
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 82 | 75.7 (13.9) |
subtype1 | 38 | 76.1 (15.7) |
subtype2 | 14 | 80.0 (11.1) |
subtype3 | 30 | 73.3 (12.4) |
P value = 0.485 (Fisher's exact test), Q value = 0.85
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 15 | 26 | 5 | 3 |
subtype1 | 10 | 12 | 3 | 2 |
subtype2 | 2 | 9 | 0 | 0 |
subtype3 | 3 | 5 | 2 | 1 |
P value = 0.774 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 10 | 327 |
subtype1 | 5 | 139 |
subtype2 | 1 | 74 |
subtype3 | 4 | 114 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 118 | 100 | 188 | 169 |
P value = 0.139 (logrank test), Q value = 0.54
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 560 | 336 | 0.3 - 180.2 (33.2) |
subtype1 | 116 | 71 | 0.3 - 153.4 (31.0) |
subtype2 | 95 | 61 | 0.8 - 116.7 (29.1) |
subtype3 | 184 | 107 | 0.3 - 180.2 (34.3) |
subtype4 | 165 | 97 | 0.8 - 152.0 (35.0) |
P value = 4.84e-12 (Kruskal-Wallis (anova)), Q value = 4.7e-10
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 554 | 59.8 (11.6) |
subtype1 | 116 | 62.9 (12.2) |
subtype2 | 95 | 62.0 (12.2) |
subtype3 | 182 | 54.4 (10.2) |
subtype4 | 161 | 62.3 (10.2) |
P value = 0.411 (Fisher's exact test), Q value = 0.84
nPatients | OMENTUM | OVARY | PERITONEUM OVARY |
---|---|---|---|
ALL | 2 | 561 | 2 |
subtype1 | 1 | 117 | 0 |
subtype2 | 0 | 97 | 0 |
subtype3 | 1 | 184 | 0 |
subtype4 | 0 | 163 | 2 |
P value = 0.012 (Fisher's exact test), Q value = 0.13
nPatients | NO | YES |
---|---|---|
ALL | 542 | 5 |
subtype1 | 111 | 3 |
subtype2 | 90 | 2 |
subtype3 | 180 | 0 |
subtype4 | 161 | 0 |
P value = 0.246 (Kruskal-Wallis (anova)), Q value = 0.7
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 75.6 (12.8) |
subtype1 | 21 | 73.3 (13.2) |
subtype2 | 15 | 73.3 (14.5) |
subtype3 | 21 | 80.0 (8.9) |
subtype4 | 21 | 75.2 (14.0) |
P value = 0.852 (Fisher's exact test), Q value = 1
nPatients | R0 | R1 | R2 |
---|---|---|---|
ALL | 14 | 26 | 2 |
subtype1 | 3 | 5 | 0 |
subtype2 | 2 | 8 | 0 |
subtype3 | 5 | 6 | 1 |
subtype4 | 4 | 7 | 1 |
P value = 0.654 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 11 | 331 |
subtype1 | 2 | 80 |
subtype2 | 1 | 57 |
subtype3 | 3 | 104 |
subtype4 | 5 | 90 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 150 | 192 | 78 |
P value = 0.0268 (logrank test), Q value = 0.2
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 416 | 247 | 0.3 - 180.2 (33.6) |
subtype1 | 147 | 94 | 0.4 - 153.4 (31.6) |
subtype2 | 191 | 103 | 0.3 - 180.2 (35.8) |
subtype3 | 78 | 50 | 1.1 - 91.7 (28.7) |
P value = 0.453 (Kruskal-Wallis (anova)), Q value = 0.84
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 413 | 59.7 (11.8) |
subtype1 | 148 | 59.9 (12.0) |
subtype2 | 189 | 59.1 (11.6) |
subtype3 | 76 | 60.8 (11.9) |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | OMENTUM | OVARY | PERITONEUM OVARY |
---|---|---|---|
ALL | 3 | 415 | 2 |
subtype1 | 1 | 148 | 1 |
subtype2 | 2 | 189 | 1 |
subtype3 | 0 | 78 | 0 |
P value = 0.532 (Fisher's exact test), Q value = 0.87
nPatients | NO | YES |
---|---|---|
ALL | 401 | 4 |
subtype1 | 141 | 2 |
subtype2 | 186 | 1 |
subtype3 | 74 | 1 |
P value = 0.481 (Kruskal-Wallis (anova)), Q value = 0.85
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 57 | 75.3 (13.5) |
subtype1 | 25 | 76.8 (12.8) |
subtype2 | 27 | 73.0 (14.1) |
subtype3 | 5 | 80.0 (14.1) |
P value = 0.314 (Fisher's exact test), Q value = 0.78
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 14 | 29 | 5 | 3 |
subtype1 | 2 | 12 | 1 | 1 |
subtype2 | 9 | 8 | 3 | 1 |
subtype3 | 3 | 9 | 1 | 1 |
P value = 0.723 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 215 |
subtype1 | 2 | 79 |
subtype2 | 5 | 98 |
subtype3 | 1 | 38 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 146 | 57 | 61 | 156 |
P value = 0.00323 (logrank test), Q value = 0.045
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 416 | 247 | 0.3 - 180.2 (33.6) |
subtype1 | 145 | 89 | 0.4 - 180.2 (30.2) |
subtype2 | 57 | 42 | 0.8 - 90.4 (34.8) |
subtype3 | 61 | 31 | 0.8 - 127.8 (36.9) |
subtype4 | 153 | 85 | 0.3 - 152.0 (35.0) |
P value = 0.0379 (Kruskal-Wallis (anova)), Q value = 0.23
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 413 | 59.7 (11.8) |
subtype1 | 144 | 59.9 (11.9) |
subtype2 | 57 | 62.8 (10.7) |
subtype3 | 61 | 57.0 (12.4) |
subtype4 | 151 | 59.4 (11.6) |
P value = 0.0526 (Fisher's exact test), Q value = 0.3
nPatients | OMENTUM | OVARY | PERITONEUM OVARY |
---|---|---|---|
ALL | 3 | 415 | 2 |
subtype1 | 1 | 145 | 0 |
subtype2 | 2 | 54 | 1 |
subtype3 | 0 | 61 | 0 |
subtype4 | 0 | 155 | 1 |
P value = 0.904 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 401 | 4 |
subtype1 | 140 | 1 |
subtype2 | 56 | 0 |
subtype3 | 59 | 1 |
subtype4 | 146 | 2 |
P value = 0.938 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 57 | 75.3 (13.5) |
subtype1 | 14 | 76.4 (16.5) |
subtype2 | 9 | 73.3 (17.3) |
subtype3 | 17 | 74.1 (11.8) |
subtype4 | 17 | 76.5 (11.1) |
P value = 0.518 (Fisher's exact test), Q value = 0.86
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 14 | 29 | 5 | 3 |
subtype1 | 4 | 13 | 3 | 0 |
subtype2 | 3 | 6 | 0 | 1 |
subtype3 | 2 | 5 | 0 | 0 |
subtype4 | 5 | 5 | 2 | 2 |
P value = 0.117 (Fisher's exact test), Q value = 0.54
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 215 |
subtype1 | 1 | 75 |
subtype2 | 2 | 25 |
subtype3 | 3 | 32 |
subtype4 | 2 | 83 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 79 | 110 | 114 |
P value = 0.791 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 302 | 183 | 0.3 - 180.2 (31.3) |
subtype1 | 78 | 44 | 0.8 - 116.1 (34.6) |
subtype2 | 110 | 69 | 0.3 - 152.0 (30.6) |
subtype3 | 114 | 70 | 0.3 - 180.2 (30.1) |
P value = 0.000846 (Kruskal-Wallis (anova)), Q value = 0.017
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 295 | 59.1 (10.9) |
subtype1 | 76 | 55.4 (10.8) |
subtype2 | 107 | 61.3 (10.5) |
subtype3 | 112 | 59.6 (10.8) |
P value = 0.784 (Fisher's exact test), Q value = 1
nPatients | OMENTUM | OVARY |
---|---|---|
ALL | 3 | 300 |
subtype1 | 0 | 79 |
subtype2 | 1 | 109 |
subtype3 | 2 | 112 |
P value = 0.199 (Fisher's exact test), Q value = 0.62
nPatients | NO | YES |
---|---|---|
ALL | 288 | 2 |
subtype1 | 75 | 0 |
subtype2 | 104 | 2 |
subtype3 | 109 | 0 |
P value = 0.427 (Kruskal-Wallis (anova)), Q value = 0.84
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 20 | 78.0 (16.1) |
subtype1 | 4 | 72.5 (22.2) |
subtype2 | 6 | 85.0 (12.2) |
subtype3 | 10 | 76.0 (15.8) |
P value = 0.51 (Fisher's exact test), Q value = 0.86
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 3 | 5 | 2 | 3 |
subtype1 | 1 | 0 | 1 | 1 |
subtype2 | 2 | 2 | 1 | 2 |
subtype3 | 0 | 3 | 0 | 0 |
P value = 0.0183 (Fisher's exact test), Q value = 0.16
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 3 | 163 |
subtype1 | 3 | 41 |
subtype2 | 0 | 60 |
subtype3 | 0 | 62 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 147 | 60 | 96 |
P value = 0.124 (logrank test), Q value = 0.54
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 302 | 183 | 0.3 - 180.2 (31.3) |
subtype1 | 146 | 83 | 0.3 - 180.2 (35.5) |
subtype2 | 60 | 40 | 1.0 - 152.0 (26.4) |
subtype3 | 96 | 60 | 0.3 - 145.4 (30.1) |
P value = 0.0145 (Kruskal-Wallis (anova)), Q value = 0.14
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 295 | 59.1 (10.9) |
subtype1 | 142 | 57.4 (10.6) |
subtype2 | 59 | 62.4 (10.8) |
subtype3 | 94 | 59.7 (11.0) |
P value = 0.59 (Fisher's exact test), Q value = 0.93
nPatients | OMENTUM | OVARY |
---|---|---|
ALL | 3 | 300 |
subtype1 | 1 | 146 |
subtype2 | 0 | 60 |
subtype3 | 2 | 94 |
P value = 0.467 (Fisher's exact test), Q value = 0.85
nPatients | NO | YES |
---|---|---|
ALL | 288 | 2 |
subtype1 | 138 | 1 |
subtype2 | 58 | 1 |
subtype3 | 92 | 0 |
P value = 0.204 (Kruskal-Wallis (anova)), Q value = 0.62
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 20 | 78.0 (16.1) |
subtype1 | 9 | 75.6 (14.2) |
subtype2 | 3 | 93.3 (11.5) |
subtype3 | 8 | 75.0 (17.7) |
P value = 0.589 (Fisher's exact test), Q value = 0.93
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 3 | 5 | 2 | 3 |
subtype1 | 1 | 3 | 1 | 2 |
subtype2 | 2 | 0 | 1 | 1 |
subtype3 | 0 | 2 | 0 | 0 |
P value = 0.326 (Fisher's exact test), Q value = 0.78
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 3 | 163 |
subtype1 | 3 | 73 |
subtype2 | 0 | 39 |
subtype3 | 0 | 51 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 74 | 135 | 141 | 103 |
P value = 0.0353 (logrank test), Q value = 0.23
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 451 | 283 | 0.3 - 180.2 (35.0) |
subtype1 | 74 | 51 | 0.3 - 152.0 (30.1) |
subtype2 | 134 | 94 | 1.0 - 153.4 (43.7) |
subtype3 | 140 | 82 | 0.3 - 130.0 (29.8) |
subtype4 | 103 | 56 | 0.3 - 180.2 (37.0) |
P value = 0.911 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 445 | 59.8 (11.5) |
subtype1 | 73 | 60.5 (12.2) |
subtype2 | 134 | 59.8 (11.4) |
subtype3 | 137 | 59.4 (12.0) |
subtype4 | 101 | 59.8 (10.5) |
P value = 0.0579 (Fisher's exact test), Q value = 0.32
nPatients | OMENTUM | OVARY | PERITONEUM OVARY |
---|---|---|---|
ALL | 2 | 450 | 1 |
subtype1 | 1 | 72 | 1 |
subtype2 | 0 | 135 | 0 |
subtype3 | 0 | 141 | 0 |
subtype4 | 1 | 102 | 0 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 438 | 3 |
subtype1 | 72 | 0 |
subtype2 | 132 | 1 |
subtype3 | 135 | 1 |
subtype4 | 99 | 1 |
P value = 0.98 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 64 | 75.3 (13.2) |
subtype1 | 6 | 76.7 (15.1) |
subtype2 | 38 | 75.8 (13.3) |
subtype3 | 8 | 72.5 (14.9) |
subtype4 | 12 | 75.0 (12.4) |
P value = 0.631 (Fisher's exact test), Q value = 0.98
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 263 |
subtype1 | 0 | 44 |
subtype2 | 4 | 89 |
subtype3 | 2 | 79 |
subtype4 | 2 | 51 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 105 | 73 | 169 | 106 |
P value = 0.15 (logrank test), Q value = 0.54
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 451 | 283 | 0.3 - 180.2 (35.0) |
subtype1 | 105 | 63 | 0.3 - 153.4 (43.9) |
subtype2 | 73 | 48 | 0.8 - 119.0 (29.2) |
subtype3 | 168 | 113 | 0.3 - 180.2 (34.8) |
subtype4 | 105 | 59 | 0.3 - 130.0 (32.5) |
P value = 0.000116 (Kruskal-Wallis (anova)), Q value = 0.0038
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 = 0.869 (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 = 0.514 (Fisher's exact test), Q value = 0.86
nPatients | NO | YES |
---|---|---|
ALL | 438 | 3 |
subtype1 | 103 | 0 |
subtype2 | 70 | 1 |
subtype3 | 162 | 2 |
subtype4 | 103 | 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 = 0.773 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 263 |
subtype1 | 3 | 70 |
subtype2 | 2 | 45 |
subtype3 | 2 | 91 |
subtype4 | 1 | 57 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 6 | 6 | 5 | 5 |
P value = 0.183 (logrank test), Q value = 0.61
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 22 | 15 | 0.8 - 125.8 (30.4) |
subtype1 | 6 | 5 | 15.8 - 55.9 (28.4) |
subtype2 | 6 | 2 | 5.4 - 115.9 (64.8) |
subtype3 | 5 | 5 | 11.1 - 67.4 (29.0) |
subtype4 | 5 | 3 | 0.8 - 125.8 (4.8) |
P value = 0.374 (Kruskal-Wallis (anova)), Q value = 0.84
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 21 | 60.5 (12.6) |
subtype1 | 6 | 56.0 (12.9) |
subtype2 | 5 | 56.0 (8.3) |
subtype3 | 5 | 64.2 (17.0) |
subtype4 | 5 | 66.6 (10.5) |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | OMENTUM | OVARY |
---|---|---|
ALL | 1 | 21 |
subtype1 | 1 | 5 |
subtype2 | 0 | 6 |
subtype3 | 0 | 5 |
subtype4 | 0 | 5 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 5 | 2 | 2 | 4 | 5 | 4 |
P value = 0.136 (logrank test), Q value = 0.54
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 18 | 12 | 0.8 - 125.8 (30.4) |
subtype1 | 5 | 4 | 15.8 - 55.9 (29.0) |
subtype4 | 4 | 1 | 5.4 - 115.9 (64.8) |
subtype5 | 5 | 4 | 0.8 - 125.8 (36.2) |
subtype6 | 4 | 3 | 1.0 - 42.0 (12.7) |
P value = 0.434 (Kruskal-Wallis (anova)), Q value = 0.84
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 17 | 59.4 (13.1) |
subtype1 | 5 | 55.6 (14.9) |
subtype4 | 3 | 52.3 (8.7) |
subtype5 | 5 | 66.4 (8.1) |
subtype6 | 4 | 60.5 (17.9) |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | OMENTUM | OVARY |
---|---|---|
ALL | 1 | 17 |
subtype1 | 0 | 5 |
subtype4 | 0 | 4 |
subtype5 | 1 | 4 |
subtype6 | 0 | 4 |
-
Cluster data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/OV-TP/22555032/OV-TP.mergedcluster.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/OV-TP/22507289/OV-TP.merged_data.txt
-
Number of patients = 589
-
Number of clustering approaches = 14
-
Number of selected clinical features = 7
-
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.