This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 12 different clustering approaches and 5 clinical features across 482 patients, 25 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 correlate to 'AGE' and 'HISTOLOGICAL.TYPE'.
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5 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes correlate to 'Time to Death', 'AGE', and 'HISTOLOGICAL.TYPE'.
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3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.
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CNMF clustering analysis on RPPA data identified 6 subtypes that correlate to 'HISTOLOGICAL.TYPE'.
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Consensus hierarchical clustering analysis on RPPA data identified 2 subtypes that correlate to 'HISTOLOGICAL.TYPE' and 'COMPLETENESS.OF.RESECTION'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'Time to Death', 'AGE', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'Time to Death', 'AGE', and 'HISTOLOGICAL.TYPE'.
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3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'Time to Death', 'AGE', and 'HISTOLOGICAL.TYPE'.
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3 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes correlate to 'Time to Death', 'AGE', and 'HISTOLOGICAL.TYPE'.
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3 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.
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3 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.
Clinical Features |
Time to Death |
AGE |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
COMPLETENESS OF RESECTION |
Statistical Tests | logrank test | ANOVA | Chi-square test | Fisher's exact test | Chi-square test |
mRNA CNMF subtypes |
0.838 (1.00) |
0.0116 (0.406) |
0.00151 (0.0605) |
0.0371 (0.991) |
0.855 (1.00) |
mRNA cHierClus subtypes |
0.71 (1.00) |
0.00301 (0.117) |
9.4e-05 (0.00423) |
0.0215 (0.645) |
0.677 (1.00) |
Copy Number Ratio CNMF subtypes |
0.000694 (0.0298) |
1.8e-09 (9.36e-08) |
5.21e-49 (3.12e-47) |
0.0182 (0.601) |
0.23 (1.00) |
METHLYATION CNMF |
0.0157 (0.534) |
0.0367 (0.991) |
7.91e-24 (4.43e-22) |
0.129 (1.00) |
0.0558 (1.00) |
RPPA CNMF subtypes |
0.0853 (1.00) |
0.203 (1.00) |
0.00103 (0.0423) |
0.461 (1.00) |
0.102 (1.00) |
RPPA cHierClus subtypes |
0.087 (1.00) |
0.236 (1.00) |
0.000814 (0.0342) |
0.46 (1.00) |
0.00347 (0.132) |
RNAseq CNMF subtypes |
1.38e-05 (0.000691) |
2.33e-05 (0.00114) |
1.1e-37 (6.47e-36) |
0.00356 (0.132) |
0.0751 (1.00) |
RNAseq cHierClus subtypes |
0.000114 (0.005) |
5.28e-05 (0.00248) |
8.53e-33 (4.86e-31) |
0.0201 (0.639) |
0.13 (1.00) |
MIRSEQ CNMF |
5.93e-05 (0.00273) |
5.79e-08 (2.95e-06) |
4.12e-37 (2.39e-35) |
0.835 (1.00) |
0.0545 (1.00) |
MIRSEQ CHIERARCHICAL |
3.41e-05 (0.00164) |
0.00545 (0.196) |
2.3e-19 (1.24e-17) |
0.964 (1.00) |
0.714 (1.00) |
MIRseq Mature CNMF subtypes |
0.02 (0.639) |
0.0844 (1.00) |
7.46e-11 (3.95e-09) |
0.332 (1.00) |
0.0301 (0.872) |
MIRseq Mature cHierClus subtypes |
0.127 (1.00) |
0.0353 (0.988) |
1.69e-19 (9.31e-18) |
0.795 (1.00) |
0.584 (1.00) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 14 | 18 | 12 | 10 |
P value = 0.838 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 54 | 9 | 6.0 - 149.6 (37.4) |
subtype1 | 14 | 2 | 13.6 - 149.6 (41.7) |
subtype2 | 18 | 4 | 6.0 - 125.4 (46.2) |
subtype3 | 12 | 1 | 19.8 - 105.4 (33.8) |
subtype4 | 10 | 2 | 7.9 - 82.5 (28.3) |
P value = 0.0116 (ANOVA), Q value = 0.41
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 54 | 62.9 (11.8) |
subtype1 | 14 | 65.6 (11.7) |
subtype2 | 18 | 68.2 (9.3) |
subtype3 | 12 | 58.7 (11.9) |
subtype4 | 10 | 54.9 (11.5) |
P value = 0.00151 (Chi-square test), Q value = 0.06
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 41 | 1 | 12 |
subtype1 | 12 | 0 | 2 |
subtype2 | 8 | 0 | 10 |
subtype3 | 11 | 1 | 0 |
subtype4 | 10 | 0 | 0 |
P value = 0.0371 (Fisher's exact test), Q value = 0.99
nPatients | NO | YES |
---|---|---|
ALL | 25 | 29 |
subtype1 | 8 | 6 |
subtype2 | 12 | 6 |
subtype3 | 3 | 9 |
subtype4 | 2 | 8 |
P value = 0.855 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 39 | 6 | 2 | 1 |
subtype1 | 8 | 2 | 1 | 0 |
subtype2 | 14 | 1 | 1 | 1 |
subtype3 | 9 | 2 | 0 | 0 |
subtype4 | 8 | 1 | 0 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 19 | 19 | 16 |
P value = 0.71 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 54 | 9 | 6.0 - 149.6 (37.4) |
subtype1 | 19 | 3 | 13.6 - 149.6 (46.5) |
subtype2 | 19 | 2 | 7.9 - 105.4 (29.7) |
subtype3 | 16 | 4 | 6.0 - 125.4 (46.2) |
P value = 0.00301 (ANOVA), Q value = 0.12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 54 | 62.9 (11.8) |
subtype1 | 19 | 63.9 (10.5) |
subtype2 | 19 | 56.4 (12.5) |
subtype3 | 16 | 69.5 (8.7) |
P value = 9.4e-05 (Chi-square test), Q value = 0.0042
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 41 | 1 | 12 |
subtype1 | 16 | 1 | 2 |
subtype2 | 19 | 0 | 0 |
subtype3 | 6 | 0 | 10 |
P value = 0.0215 (Fisher's exact test), Q value = 0.65
nPatients | NO | YES |
---|---|---|
ALL | 25 | 29 |
subtype1 | 11 | 8 |
subtype2 | 4 | 15 |
subtype3 | 10 | 6 |
P value = 0.677 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 39 | 6 | 2 | 1 |
subtype1 | 13 | 2 | 1 | 0 |
subtype2 | 13 | 3 | 0 | 0 |
subtype3 | 13 | 1 | 1 | 1 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 281 | 45 | 132 | 11 | 5 |
P value = 0.000694 (logrank test), Q value = 0.03
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 472 | 59 | 0.0 - 191.8 (21.5) |
subtype1 | 280 | 23 | 0.1 - 191.8 (24.1) |
subtype2 | 45 | 9 | 0.2 - 149.6 (17.6) |
subtype3 | 131 | 26 | 0.0 - 125.4 (17.6) |
subtype4 | 11 | 1 | 8.7 - 73.2 (33.4) |
subtype5 | 5 | 0 | 19.3 - 45.8 (29.9) |
P value = 1.8e-09 (ANOVA), Q value = 9.4e-08
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 473 | 63.8 (11.3) |
subtype1 | 280 | 61.3 (11.1) |
subtype2 | 45 | 62.5 (12.4) |
subtype3 | 132 | 69.2 (8.8) |
subtype4 | 11 | 63.3 (14.0) |
subtype5 | 5 | 67.2 (12.7) |
P value = 5.21e-49 (Chi-square test), Q value = 3.1e-47
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 362 | 19 | 93 |
subtype1 | 269 | 7 | 5 |
subtype2 | 41 | 0 | 4 |
subtype3 | 38 | 10 | 84 |
subtype4 | 10 | 1 | 0 |
subtype5 | 4 | 1 | 0 |
P value = 0.0182 (Chi-square test), Q value = 0.6
nPatients | NO | YES |
---|---|---|
ALL | 135 | 339 |
subtype1 | 94 | 187 |
subtype2 | 6 | 39 |
subtype3 | 29 | 103 |
subtype4 | 4 | 7 |
subtype5 | 2 | 3 |
P value = 0.23 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 327 | 24 | 16 | 27 |
subtype1 | 200 | 15 | 4 | 15 |
subtype2 | 31 | 1 | 2 | 3 |
subtype3 | 83 | 8 | 10 | 9 |
subtype4 | 8 | 0 | 0 | 0 |
subtype5 | 5 | 0 | 0 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 131 | 81 | 154 |
P value = 0.0157 (logrank test), Q value = 0.53
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 364 | 44 | 0.0 - 191.8 (17.6) |
subtype1 | 129 | 24 | 0.0 - 191.8 (15.8) |
subtype2 | 81 | 6 | 0.1 - 102.3 (19.4) |
subtype3 | 154 | 14 | 0.1 - 185.8 (17.9) |
P value = 0.0367 (ANOVA), Q value = 0.99
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 365 | 63.9 (11.3) |
subtype1 | 130 | 65.9 (10.6) |
subtype2 | 81 | 63.4 (12.9) |
subtype3 | 154 | 62.5 (10.9) |
P value = 7.91e-24 (Chi-square test), Q value = 4.4e-22
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 270 | 18 | 78 |
subtype1 | 56 | 13 | 62 |
subtype2 | 63 | 2 | 16 |
subtype3 | 151 | 3 | 0 |
P value = 0.129 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 84 | 282 |
subtype1 | 34 | 97 |
subtype2 | 12 | 69 |
subtype3 | 38 | 116 |
P value = 0.0558 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 243 | 18 | 12 | 26 |
subtype1 | 83 | 8 | 7 | 10 |
subtype2 | 51 | 4 | 4 | 10 |
subtype3 | 109 | 6 | 1 | 6 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 42 | 39 | 40 | 12 | 41 | 26 |
P value = 0.0853 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 200 | 20 | 0.6 - 185.8 (29.2) |
subtype1 | 42 | 4 | 0.6 - 106.9 (29.5) |
subtype2 | 39 | 6 | 6.0 - 149.6 (28.1) |
subtype3 | 40 | 1 | 1.8 - 185.8 (29.9) |
subtype4 | 12 | 4 | 1.4 - 87.3 (35.6) |
subtype5 | 41 | 2 | 0.7 - 113.4 (24.6) |
subtype6 | 26 | 3 | 0.7 - 78.2 (29.6) |
P value = 0.203 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 200 | 62.7 (11.1) |
subtype1 | 42 | 62.3 (12.7) |
subtype2 | 39 | 64.2 (9.6) |
subtype3 | 40 | 62.2 (11.2) |
subtype4 | 12 | 69.8 (8.5) |
subtype5 | 41 | 60.7 (9.4) |
subtype6 | 26 | 62.0 (12.8) |
P value = 0.00103 (Chi-square test), Q value = 0.042
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 174 | 3 | 23 |
subtype1 | 35 | 1 | 6 |
subtype2 | 28 | 0 | 11 |
subtype3 | 39 | 1 | 0 |
subtype4 | 12 | 0 | 0 |
subtype5 | 41 | 0 | 0 |
subtype6 | 19 | 1 | 6 |
P value = 0.461 (Chi-square test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 80 | 120 |
subtype1 | 20 | 22 |
subtype2 | 19 | 20 |
subtype3 | 13 | 27 |
subtype4 | 4 | 8 |
subtype5 | 13 | 28 |
subtype6 | 11 | 15 |
P value = 0.102 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 141 | 9 | 5 | 16 |
subtype1 | 24 | 3 | 3 | 6 |
subtype2 | 29 | 1 | 1 | 2 |
subtype3 | 26 | 0 | 0 | 5 |
subtype4 | 10 | 1 | 1 | 0 |
subtype5 | 30 | 4 | 0 | 1 |
subtype6 | 22 | 0 | 0 | 2 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 124 | 76 |
P value = 0.087 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 200 | 20 | 0.6 - 185.8 (29.2) |
subtype1 | 124 | 9 | 0.7 - 185.8 (29.9) |
subtype2 | 76 | 11 | 0.6 - 149.6 (23.9) |
P value = 0.236 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 200 | 62.7 (11.1) |
subtype1 | 124 | 62.0 (10.9) |
subtype2 | 76 | 63.9 (11.3) |
P value = 0.000814 (Chi-square test), Q value = 0.034
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 174 | 3 | 23 |
subtype1 | 116 | 2 | 6 |
subtype2 | 58 | 1 | 17 |
P value = 0.46 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 80 | 120 |
subtype1 | 47 | 77 |
subtype2 | 33 | 43 |
P value = 0.00347 (Chi-square test), Q value = 0.13
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 141 | 9 | 5 | 16 |
subtype1 | 94 | 6 | 0 | 6 |
subtype2 | 47 | 3 | 5 | 10 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 198 | 142 | 137 |
P value = 1.38e-05 (logrank test), Q value = 0.00069
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 475 | 59 | 0.0 - 191.8 (20.9) |
subtype1 | 196 | 40 | 0.0 - 191.8 (17.9) |
subtype2 | 142 | 12 | 0.3 - 185.8 (26.7) |
subtype3 | 137 | 7 | 0.1 - 113.4 (23.9) |
P value = 2.33e-05 (ANOVA), Q value = 0.0011
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 476 | 63.7 (11.2) |
subtype1 | 197 | 66.3 (10.7) |
subtype2 | 142 | 60.7 (11.2) |
subtype3 | 137 | 63.2 (11.3) |
P value = 1.1e-37 (Chi-square test), Q value = 6.5e-36
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 365 | 18 | 94 |
subtype1 | 91 | 14 | 93 |
subtype2 | 141 | 1 | 0 |
subtype3 | 133 | 3 | 1 |
P value = 0.00356 (Fisher's exact test), Q value = 0.13
nPatients | NO | YES |
---|---|---|
ALL | 134 | 343 |
subtype1 | 49 | 149 |
subtype2 | 55 | 87 |
subtype3 | 30 | 107 |
P value = 0.0751 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 328 | 24 | 16 | 27 |
subtype1 | 126 | 13 | 11 | 13 |
subtype2 | 105 | 7 | 3 | 4 |
subtype3 | 97 | 4 | 2 | 10 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 140 | 124 | 213 |
P value = 0.000114 (logrank test), Q value = 0.005
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 475 | 59 | 0.0 - 191.8 (20.9) |
subtype1 | 140 | 7 | 0.1 - 113.4 (24.3) |
subtype2 | 124 | 12 | 0.7 - 185.8 (25.1) |
subtype3 | 211 | 40 | 0.0 - 191.8 (17.9) |
P value = 5.28e-05 (ANOVA), Q value = 0.0025
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 476 | 63.7 (11.2) |
subtype1 | 140 | 63.0 (11.2) |
subtype2 | 124 | 60.5 (11.6) |
subtype3 | 212 | 66.0 (10.6) |
P value = 8.53e-33 (Chi-square test), Q value = 4.9e-31
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 365 | 18 | 94 |
subtype1 | 136 | 3 | 1 |
subtype2 | 123 | 1 | 0 |
subtype3 | 106 | 14 | 93 |
P value = 0.0201 (Fisher's exact test), Q value = 0.64
nPatients | NO | YES |
---|---|---|
ALL | 134 | 343 |
subtype1 | 33 | 107 |
subtype2 | 47 | 77 |
subtype3 | 54 | 159 |
P value = 0.13 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 328 | 24 | 16 | 27 |
subtype1 | 101 | 3 | 2 | 10 |
subtype2 | 88 | 8 | 3 | 4 |
subtype3 | 139 | 13 | 11 | 13 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 179 | 157 | 137 |
P value = 5.93e-05 (logrank test), Q value = 0.0027
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 471 | 56 | 0.0 - 191.8 (21.2) |
subtype1 | 177 | 34 | 0.0 - 191.8 (17.9) |
subtype2 | 157 | 7 | 0.1 - 113.4 (24.4) |
subtype3 | 137 | 15 | 0.2 - 185.8 (25.0) |
P value = 5.79e-08 (ANOVA), Q value = 3e-06
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 472 | 63.7 (11.3) |
subtype1 | 178 | 67.1 (10.0) |
subtype2 | 157 | 62.9 (11.1) |
subtype3 | 137 | 60.0 (11.7) |
P value = 4.12e-37 (Chi-square test), Q value = 2.4e-35
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 365 | 19 | 89 |
subtype1 | 80 | 14 | 85 |
subtype2 | 154 | 1 | 2 |
subtype3 | 131 | 4 | 2 |
P value = 0.835 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 131 | 342 |
subtype1 | 47 | 132 |
subtype2 | 44 | 113 |
subtype3 | 40 | 97 |
P value = 0.0545 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 325 | 24 | 15 | 27 |
subtype1 | 115 | 11 | 11 | 11 |
subtype2 | 117 | 4 | 2 | 9 |
subtype3 | 93 | 9 | 2 | 7 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 7 | 211 | 255 |
P value = 3.41e-05 (logrank test), Q value = 0.0016
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 471 | 56 | 0.0 - 191.8 (21.2) |
subtype1 | 7 | 2 | 1.2 - 36.8 (17.9) |
subtype2 | 211 | 11 | 0.1 - 185.8 (24.8) |
subtype3 | 253 | 43 | 0.0 - 191.8 (18.8) |
P value = 0.00545 (ANOVA), Q value = 0.2
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 472 | 63.7 (11.3) |
subtype1 | 7 | 71.7 (14.8) |
subtype2 | 211 | 62.0 (11.3) |
subtype3 | 254 | 64.8 (11.0) |
P value = 2.3e-19 (Chi-square test), Q value = 1.2e-17
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 365 | 19 | 89 |
subtype1 | 7 | 0 | 0 |
subtype2 | 205 | 3 | 3 |
subtype3 | 153 | 16 | 86 |
P value = 0.964 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 131 | 342 |
subtype1 | 2 | 5 |
subtype2 | 59 | 152 |
subtype3 | 70 | 185 |
P value = 0.714 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 325 | 24 | 15 | 27 |
subtype1 | 3 | 0 | 0 | 0 |
subtype2 | 146 | 9 | 4 | 14 |
subtype3 | 176 | 15 | 11 | 13 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 150 | 114 | 82 |
P value = 0.02 (logrank test), Q value = 0.64
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 344 | 45 | 0.0 - 191.8 (17.0) |
subtype1 | 148 | 26 | 0.0 - 191.8 (14.7) |
subtype2 | 114 | 7 | 0.1 - 113.4 (19.8) |
subtype3 | 82 | 12 | 0.1 - 92.0 (24.2) |
P value = 0.0844 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 345 | 64.3 (11.2) |
subtype1 | 149 | 65.8 (11.2) |
subtype2 | 114 | 63.5 (10.0) |
subtype3 | 82 | 62.7 (12.6) |
P value = 7.46e-11 (Chi-square test), Q value = 4e-09
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 252 | 17 | 77 |
subtype1 | 86 | 9 | 55 |
subtype2 | 110 | 2 | 2 |
subtype3 | 56 | 6 | 20 |
P value = 0.332 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 82 | 264 |
subtype1 | 31 | 119 |
subtype2 | 27 | 87 |
subtype3 | 24 | 58 |
P value = 0.0301 (Chi-square test), Q value = 0.87
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 234 | 17 | 12 | 21 |
subtype1 | 96 | 9 | 10 | 6 |
subtype2 | 74 | 4 | 2 | 11 |
subtype3 | 64 | 4 | 0 | 4 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 26 | 173 | 147 |
P value = 0.127 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 344 | 45 | 0.0 - 191.8 (17.0) |
subtype1 | 26 | 3 | 0.2 - 113.4 (14.8) |
subtype2 | 171 | 29 | 0.0 - 191.8 (16.7) |
subtype3 | 147 | 13 | 0.1 - 88.3 (19.3) |
P value = 0.0353 (ANOVA), Q value = 0.99
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 345 | 64.3 (11.2) |
subtype1 | 26 | 62.6 (14.1) |
subtype2 | 172 | 65.8 (10.6) |
subtype3 | 147 | 62.7 (11.2) |
P value = 1.69e-19 (Chi-square test), Q value = 9.3e-18
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 252 | 17 | 77 |
subtype1 | 23 | 2 | 1 |
subtype2 | 87 | 12 | 74 |
subtype3 | 142 | 3 | 2 |
P value = 0.795 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 82 | 264 |
subtype1 | 7 | 19 |
subtype2 | 39 | 134 |
subtype3 | 36 | 111 |
P value = 0.584 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 234 | 17 | 12 | 21 |
subtype1 | 15 | 1 | 1 | 1 |
subtype2 | 118 | 11 | 8 | 8 |
subtype3 | 101 | 5 | 3 | 12 |
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Cluster data file = UCEC-TP.mergedcluster.txt
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Clinical data file = UCEC-TP.merged_data.txt
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Number of patients = 482
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Number of clustering approaches = 12
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Number of selected clinical features = 5
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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
For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between two tumor subtypes using 't.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.