This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 10 different clustering approaches and 5 clinical features across 455 patients, 20 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 '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 6 subtypes that correlate to 'HISTOLOGICAL.TYPE'.
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CNMF 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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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that correlate to 'AGE', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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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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6 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes correlate to 'Time to Death', 'AGE', and 'HISTOLOGICAL.TYPE'.
Clinical Features |
Time to Death |
AGE |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
COMPLETENESS OF RESECTION |
Statistical Tests | logrank test | ANOVA | Chi-square test | Chi-square test | Chi-square test |
mRNA CNMF subtypes |
0.942 (1.00) |
0.0107 (0.311) |
0.000456 (0.0169) |
0.0317 (0.824) |
0.847 (1.00) |
mRNA cHierClus subtypes |
0.942 (1.00) |
0.0598 (1.00) |
0.00134 (0.0457) |
0.0666 (1.00) |
0.673 (1.00) |
Copy Number Ratio CNMF subtypes |
0.00666 (0.213) |
2.51e-10 (1.1e-08) |
4.34e-42 (2.17e-40) |
0.09 (1.00) |
0.126 (1.00) |
METHLYATION CNMF |
0.023 (0.621) |
0.06 (1.00) |
1.37e-21 (6.32e-20) |
0.202 (1.00) |
0.00993 (0.298) |
RPPA CNMF subtypes |
0.778 (1.00) |
0.343 (1.00) |
5.17e-05 (0.00202) |
0.327 (1.00) |
0.12 (1.00) |
RPPA cHierClus subtypes |
0.954 (1.00) |
0.463 (1.00) |
0.000529 (0.0191) |
0.584 (1.00) |
0.0695 (1.00) |
RNAseq CNMF subtypes |
0.00308 (0.102) |
1.1e-06 (4.52e-05) |
4.3e-26 (2.02e-24) |
0.0553 (1.00) |
0.176 (1.00) |
RNAseq cHierClus subtypes |
0.099 (1.00) |
8.03e-07 (3.37e-05) |
1.47e-19 (6.62e-18) |
0.00715 (0.222) |
0.231 (1.00) |
MIRSEQ CNMF |
0.000861 (0.0301) |
2.37e-07 (1.02e-05) |
3.98e-31 (1.91e-29) |
0.329 (1.00) |
0.192 (1.00) |
MIRSEQ CHIERARCHICAL |
0.000181 (0.00689) |
1.12e-06 (4.52e-05) |
1.91e-39 (9.38e-38) |
0.016 (0.448) |
0.449 (1.00) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 13 | 19 | 14 | 8 |
P value = 0.942 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 54 | 7 | 6.0 - 133.2 (35.4) |
subtype1 | 13 | 2 | 9.0 - 133.2 (39.0) |
subtype2 | 19 | 3 | 6.0 - 113.2 (37.7) |
subtype3 | 14 | 1 | 8.6 - 89.3 (30.9) |
subtype4 | 8 | 1 | 6.4 - 65.5 (22.9) |
P value = 0.0107 (ANOVA), Q value = 0.31
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 54 | 62.9 (11.8) |
subtype1 | 13 | 65.1 (12.0) |
subtype2 | 19 | 68.4 (9.1) |
subtype3 | 14 | 58.2 (11.0) |
subtype4 | 8 | 54.8 (12.9) |
P value = 0.000456 (Chi-square test), Q value = 0.017
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 41 | 1 | 12 |
subtype1 | 12 | 0 | 1 |
subtype2 | 8 | 0 | 11 |
subtype3 | 13 | 1 | 0 |
subtype4 | 8 | 0 | 0 |
P value = 0.0317 (Fisher's exact test), Q value = 0.82
nPatients | NO | YES |
---|---|---|
ALL | 25 | 29 |
subtype1 | 7 | 6 |
subtype2 | 13 | 6 |
subtype3 | 3 | 11 |
subtype4 | 2 | 6 |
P value = 0.847 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 39 | 6 | 2 | 1 |
subtype1 | 7 | 2 | 1 | 0 |
subtype2 | 15 | 1 | 1 | 1 |
subtype3 | 11 | 2 | 0 | 0 |
subtype4 | 6 | 1 | 0 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 20 | 15 | 19 |
P value = 0.942 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 54 | 7 | 6.0 - 133.2 (35.4) |
subtype1 | 20 | 2 | 6.4 - 89.3 (29.8) |
subtype2 | 15 | 2 | 9.0 - 133.2 (39.0) |
subtype3 | 19 | 3 | 6.0 - 113.2 (37.7) |
P value = 0.0598 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 54 | 62.9 (11.8) |
subtype1 | 20 | 58.2 (13.3) |
subtype2 | 15 | 64.0 (10.6) |
subtype3 | 19 | 67.1 (9.9) |
P value = 0.00134 (Chi-square test), Q value = 0.046
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 41 | 1 | 12 |
subtype1 | 19 | 1 | 0 |
subtype2 | 13 | 0 | 2 |
subtype3 | 9 | 0 | 10 |
P value = 0.0666 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 25 | 29 |
subtype1 | 5 | 15 |
subtype2 | 9 | 6 |
subtype3 | 11 | 8 |
P value = 0.673 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 39 | 6 | 2 | 1 |
subtype1 | 14 | 3 | 0 | 0 |
subtype2 | 10 | 2 | 1 | 0 |
subtype3 | 15 | 1 | 1 | 1 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 275 | 38 | 112 | 16 | 6 |
P value = 0.00666 (logrank test), Q value = 0.21
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 442 | 41 | 0.0 - 187.1 (15.9) |
subtype1 | 272 | 18 | 0.0 - 187.1 (17.3) |
subtype2 | 38 | 4 | 0.2 - 133.2 (8.3) |
subtype3 | 110 | 15 | 0.0 - 113.2 (13.3) |
subtype4 | 16 | 4 | 1.7 - 33.5 (13.9) |
subtype5 | 6 | 0 | 0.3 - 31.3 (18.6) |
P value = 2.51e-10 (ANOVA), Q value = 1.1e-08
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 446 | 63.6 (11.3) |
subtype1 | 274 | 61.2 (11.1) |
subtype2 | 38 | 63.1 (11.8) |
subtype3 | 112 | 69.6 (8.3) |
subtype4 | 16 | 60.2 (12.9) |
subtype5 | 6 | 71.0 (14.7) |
P value = 4.34e-42 (Chi-square test), Q value = 2.2e-40
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 350 | 18 | 79 |
subtype1 | 262 | 8 | 5 |
subtype2 | 34 | 0 | 4 |
subtype3 | 35 | 8 | 69 |
subtype4 | 14 | 1 | 1 |
subtype5 | 5 | 1 | 0 |
P value = 0.09 (Chi-square test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 133 | 314 |
subtype1 | 94 | 181 |
subtype2 | 6 | 32 |
subtype3 | 27 | 85 |
subtype4 | 4 | 12 |
subtype5 | 2 | 4 |
P value = 0.126 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 307 | 24 | 15 | 24 |
subtype1 | 194 | 15 | 4 | 14 |
subtype2 | 26 | 1 | 1 | 3 |
subtype3 | 71 | 8 | 8 | 7 |
subtype4 | 10 | 0 | 2 | 0 |
subtype5 | 6 | 0 | 0 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 120 | 74 | 144 |
P value = 0.023 (logrank test), Q value = 0.62
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 333 | 31 | 0.0 - 187.1 (12.4) |
subtype1 | 117 | 18 | 0.0 - 187.1 (11.4) |
subtype2 | 74 | 4 | 0.0 - 92.0 (16.8) |
subtype3 | 142 | 9 | 0.1 - 173.6 (12.3) |
P value = 0.06 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 337 | 63.7 (11.3) |
subtype1 | 119 | 65.6 (10.6) |
subtype2 | 74 | 63.2 (13.1) |
subtype3 | 144 | 62.3 (10.8) |
P value = 1.37e-21 (Chi-square test), Q value = 6.3e-20
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 258 | 17 | 63 |
subtype1 | 55 | 12 | 53 |
subtype2 | 61 | 3 | 10 |
subtype3 | 142 | 2 | 0 |
P value = 0.202 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 81 | 257 |
subtype1 | 32 | 88 |
subtype2 | 12 | 62 |
subtype3 | 37 | 107 |
P value = 0.00993 (Chi-square test), Q value = 0.3
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 223 | 18 | 11 | 22 |
subtype1 | 76 | 8 | 7 | 7 |
subtype2 | 47 | 4 | 3 | 11 |
subtype3 | 100 | 6 | 1 | 4 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 41 | 38 | 41 | 16 | 38 | 26 |
P value = 0.778 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 200 | 13 | 0.0 - 173.6 (21.7) |
subtype1 | 41 | 4 | 0.6 - 106.9 (21.0) |
subtype2 | 38 | 2 | 1.3 - 133.2 (24.7) |
subtype3 | 41 | 2 | 1.8 - 173.6 (22.6) |
subtype4 | 16 | 2 | 1.4 - 82.7 (26.6) |
subtype5 | 38 | 1 | 0.0 - 101.1 (12.4) |
subtype6 | 26 | 2 | 0.7 - 66.9 (20.8) |
P value = 0.343 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 200 | 62.7 (11.1) |
subtype1 | 41 | 62.9 (12.2) |
subtype2 | 38 | 63.4 (10.6) |
subtype3 | 41 | 61.9 (10.8) |
subtype4 | 16 | 68.1 (8.2) |
subtype5 | 38 | 60.6 (9.6) |
subtype6 | 26 | 62.6 (13.3) |
P value = 5.17e-05 (Chi-square test), Q value = 0.002
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 174 | 3 | 23 |
subtype1 | 34 | 1 | 6 |
subtype2 | 27 | 0 | 11 |
subtype3 | 41 | 0 | 0 |
subtype4 | 16 | 0 | 0 |
subtype5 | 38 | 0 | 0 |
subtype6 | 18 | 2 | 6 |
P value = 0.327 (Chi-square test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 80 | 120 |
subtype1 | 20 | 21 |
subtype2 | 18 | 20 |
subtype3 | 13 | 28 |
subtype4 | 4 | 12 |
subtype5 | 13 | 25 |
subtype6 | 12 | 14 |
P value = 0.12 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 141 | 9 | 5 | 16 |
subtype1 | 24 | 2 | 3 | 6 |
subtype2 | 27 | 2 | 1 | 2 |
subtype3 | 27 | 0 | 0 | 5 |
subtype4 | 13 | 1 | 1 | 1 |
subtype5 | 28 | 4 | 0 | 0 |
subtype6 | 22 | 0 | 0 | 2 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 7 | 33 | 39 | 39 | 56 | 26 |
P value = 0.954 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 200 | 13 | 0.0 - 173.6 (21.7) |
subtype1 | 7 | 0 | 9.2 - 70.4 (15.1) |
subtype2 | 33 | 2 | 0.0 - 89.3 (12.2) |
subtype3 | 39 | 2 | 0.7 - 98.2 (16.3) |
subtype4 | 39 | 4 | 1.3 - 133.2 (23.3) |
subtype5 | 56 | 3 | 1.4 - 173.6 (23.7) |
subtype6 | 26 | 2 | 0.7 - 101.1 (22.7) |
P value = 0.463 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 200 | 62.7 (11.1) |
subtype1 | 7 | 65.0 (17.0) |
subtype2 | 33 | 62.5 (11.5) |
subtype3 | 39 | 59.8 (9.3) |
subtype4 | 39 | 65.0 (11.3) |
subtype5 | 56 | 63.1 (9.8) |
subtype6 | 26 | 62.5 (13.2) |
P value = 0.000529 (Chi-square test), Q value = 0.019
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 174 | 3 | 23 |
subtype1 | 7 | 0 | 0 |
subtype2 | 29 | 1 | 3 |
subtype3 | 36 | 1 | 2 |
subtype4 | 26 | 0 | 13 |
subtype5 | 55 | 1 | 0 |
subtype6 | 21 | 0 | 5 |
P value = 0.584 (Chi-square test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 80 | 120 |
subtype1 | 2 | 5 |
subtype2 | 10 | 23 |
subtype3 | 15 | 24 |
subtype4 | 19 | 20 |
subtype5 | 25 | 31 |
subtype6 | 9 | 17 |
P value = 0.0695 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 141 | 9 | 5 | 16 |
subtype1 | 5 | 0 | 0 | 1 |
subtype2 | 21 | 1 | 1 | 6 |
subtype3 | 28 | 5 | 0 | 0 |
subtype4 | 24 | 2 | 3 | 3 |
subtype5 | 43 | 1 | 1 | 4 |
subtype6 | 20 | 0 | 0 | 2 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 142 | 113 | 114 |
P value = 0.00308 (logrank test), Q value = 0.1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 367 | 32 | 0.0 - 187.1 (17.9) |
subtype1 | 141 | 21 | 0.1 - 187.1 (15.3) |
subtype2 | 112 | 3 | 0.3 - 101.1 (17.8) |
subtype3 | 114 | 8 | 0.0 - 173.6 (22.7) |
P value = 1.1e-06 (ANOVA), Q value = 4.5e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 369 | 63.2 (11.0) |
subtype1 | 142 | 66.3 (10.0) |
subtype2 | 113 | 63.4 (10.8) |
subtype3 | 114 | 59.2 (11.2) |
P value = 4.3e-26 (Chi-square test), Q value = 2e-24
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 302 | 10 | 57 |
subtype1 | 76 | 9 | 57 |
subtype2 | 112 | 1 | 0 |
subtype3 | 114 | 0 | 0 |
P value = 0.0553 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 123 | 246 |
subtype1 | 55 | 87 |
subtype2 | 28 | 85 |
subtype3 | 40 | 74 |
P value = 0.176 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 261 | 21 | 12 | 22 |
subtype1 | 96 | 12 | 8 | 10 |
subtype2 | 80 | 4 | 2 | 8 |
subtype3 | 85 | 5 | 2 | 4 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 65 | 98 | 65 | 141 |
P value = 0.099 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 367 | 32 | 0.0 - 187.1 (17.9) |
subtype1 | 64 | 6 | 0.0 - 173.6 (17.5) |
subtype2 | 98 | 2 | 0.3 - 101.1 (17.0) |
subtype3 | 65 | 8 | 0.3 - 106.9 (25.0) |
subtype4 | 140 | 16 | 0.1 - 187.1 (16.5) |
P value = 8.03e-07 (ANOVA), Q value = 3.4e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 369 | 63.2 (11.0) |
subtype1 | 65 | 58.3 (10.4) |
subtype2 | 98 | 62.8 (10.9) |
subtype3 | 65 | 61.1 (11.5) |
subtype4 | 141 | 66.8 (10.0) |
P value = 1.47e-19 (Chi-square test), Q value = 6.6e-18
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 302 | 10 | 57 |
subtype1 | 65 | 0 | 0 |
subtype2 | 97 | 1 | 0 |
subtype3 | 60 | 2 | 3 |
subtype4 | 80 | 7 | 54 |
P value = 0.00715 (Fisher's exact test), Q value = 0.22
nPatients | NO | YES |
---|---|---|
ALL | 123 | 246 |
subtype1 | 18 | 47 |
subtype2 | 25 | 73 |
subtype3 | 33 | 32 |
subtype4 | 47 | 94 |
P value = 0.231 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 261 | 21 | 12 | 22 |
subtype1 | 48 | 4 | 1 | 4 |
subtype2 | 72 | 1 | 1 | 7 |
subtype3 | 47 | 5 | 2 | 2 |
subtype4 | 94 | 11 | 8 | 9 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 158 | 147 | 137 |
P value = 0.000861 (logrank test), Q value = 0.03
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 437 | 39 | 0.0 - 187.1 (15.8) |
subtype1 | 155 | 23 | 0.0 - 187.1 (12.4) |
subtype2 | 146 | 3 | 0.1 - 101.1 (14.8) |
subtype3 | 136 | 13 | 0.2 - 173.6 (19.5) |
P value = 2.37e-07 (ANOVA), Q value = 1e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 441 | 63.5 (11.3) |
subtype1 | 157 | 67.2 (10.3) |
subtype2 | 147 | 62.5 (11.2) |
subtype3 | 137 | 60.3 (11.2) |
P value = 3.98e-31 (Chi-square test), Q value = 1.9e-29
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 349 | 18 | 75 |
subtype1 | 75 | 14 | 69 |
subtype2 | 144 | 1 | 2 |
subtype3 | 130 | 3 | 4 |
P value = 0.329 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 127 | 315 |
subtype1 | 42 | 116 |
subtype2 | 39 | 108 |
subtype3 | 46 | 91 |
P value = 0.192 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 302 | 24 | 14 | 24 |
subtype1 | 104 | 11 | 9 | 8 |
subtype2 | 106 | 4 | 2 | 9 |
subtype3 | 92 | 9 | 3 | 7 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 51 | 119 | 74 | 20 | 35 | 143 |
P value = 0.000181 (logrank test), Q value = 0.0069
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 437 | 39 | 0.0 - 187.1 (15.8) |
subtype1 | 50 | 1 | 0.5 - 98.2 (23.0) |
subtype2 | 117 | 20 | 0.0 - 187.1 (12.4) |
subtype3 | 74 | 5 | 0.0 - 173.6 (18.6) |
subtype4 | 20 | 4 | 0.6 - 59.7 (13.4) |
subtype5 | 34 | 5 | 0.2 - 113.2 (12.8) |
subtype6 | 142 | 4 | 0.1 - 101.1 (14.1) |
P value = 1.12e-06 (ANOVA), Q value = 4.5e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 441 | 63.5 (11.3) |
subtype1 | 51 | 63.9 (10.7) |
subtype2 | 118 | 67.0 (9.5) |
subtype3 | 74 | 57.6 (12.5) |
subtype4 | 20 | 59.6 (10.3) |
subtype5 | 35 | 65.0 (13.1) |
subtype6 | 143 | 63.7 (10.6) |
P value = 1.91e-39 (Chi-square test), Q value = 9.4e-38
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 349 | 18 | 75 |
subtype1 | 49 | 1 | 1 |
subtype2 | 40 | 12 | 67 |
subtype3 | 74 | 0 | 0 |
subtype4 | 20 | 0 | 0 |
subtype5 | 30 | 2 | 3 |
subtype6 | 136 | 3 | 4 |
P value = 0.016 (Chi-square test), Q value = 0.45
nPatients | NO | YES |
---|---|---|
ALL | 127 | 315 |
subtype1 | 21 | 30 |
subtype2 | 32 | 87 |
subtype3 | 18 | 56 |
subtype4 | 11 | 9 |
subtype5 | 6 | 29 |
subtype6 | 39 | 104 |
P value = 0.449 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 302 | 24 | 14 | 24 |
subtype1 | 35 | 4 | 1 | 0 |
subtype2 | 78 | 8 | 7 | 7 |
subtype3 | 52 | 6 | 1 | 5 |
subtype4 | 13 | 0 | 1 | 2 |
subtype5 | 23 | 3 | 1 | 2 |
subtype6 | 101 | 3 | 3 | 8 |
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Cluster data file = UCEC-TP.mergedcluster.txt
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Clinical data file = UCEC-TP.clin.merged.picked.txt
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Number of patients = 455
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Number of clustering approaches = 10
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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 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.