(primary solid tumor cohort)
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, 21 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 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', 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 (0.301) |
0.000456 (0.0173) |
0.0317 (0.792) |
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 |
0.0067 (0.208) |
2.51e-10 (1.1e-08) |
4.34e-42 (2.17e-40) |
0.09 (1.00) |
0.126 (1.00) |
METHLYATION CNMF |
0.023 (0.598) |
0.06 (1.00) |
1.37e-21 (6.32e-20) |
0.202 (1.00) |
0.00993 (0.288) |
RPPA CNMF subtypes |
0.586 (1.00) |
0.203 (1.00) |
0.00103 (0.0361) |
0.461 (1.00) |
0.102 (1.00) |
RPPA cHierClus subtypes |
0.263 (1.00) |
0.236 (1.00) |
0.000814 (0.0301) |
0.46 (1.00) |
0.00347 (0.111) |
RNAseq CNMF subtypes |
0.00311 (0.103) |
1.1e-06 (4.52e-05) |
4.3e-26 (2.02e-24) |
0.0553 (1.00) |
0.176 (1.00) |
RNAseq cHierClus subtypes |
0.0994 (1.00) |
8.03e-07 (3.37e-05) |
1.47e-19 (6.62e-18) |
0.00715 (0.214) |
0.231 (1.00) |
MIRSEQ CNMF |
0.00087 (0.0313) |
2.37e-07 (1.02e-05) |
3.98e-31 (1.91e-29) |
0.329 (1.00) |
0.192 (1.00) |
MIRSEQ CHIERARCHICAL |
0.000184 (0.00716) |
1.12e-06 (4.52e-05) |
1.91e-39 (9.38e-38) |
0.016 (0.432) |
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 = 0.3
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 = 0.79
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 = 0.0067 (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 = 0.6
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 = 0.29
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 | 42 | 39 | 40 | 12 | 41 | 26 |
P value = 0.586 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 200 | 13 | 0.0 - 173.6 (21.7) |
subtype1 | 42 | 4 | 0.6 - 106.9 (21.7) |
subtype2 | 39 | 3 | 1.3 - 133.2 (23.3) |
subtype3 | 40 | 1 | 1.8 - 173.6 (22.8) |
subtype4 | 12 | 2 | 1.4 - 82.7 (26.6) |
subtype5 | 41 | 1 | 0.0 - 101.1 (13.3) |
subtype6 | 26 | 2 | 0.7 - 66.9 (22.7) |
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 = 0.036
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 = 0.263 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 200 | 13 | 0.0 - 173.6 (21.7) |
subtype1 | 124 | 6 | 0.7 - 173.6 (21.8) |
subtype2 | 76 | 7 | 0.0 - 133.2 (21.5) |
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 = 0.03
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 = 0.11
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 | 142 | 113 | 114 |
P value = 0.00311 (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 = 0.0994 (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 = 0.21
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 = 0.00087 (logrank test), Q value = 0.031
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 = 0.000184 (logrank test), Q value = 0.0072
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 = 0.43
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 |
-
Cluster data file = UCEC-TP.mergedcluster.txt
-
Clinical data file = UCEC-TP.clin.merged.picked.txt
-
Number of patients = 455
-
Number of clustering approaches = 10
-
Number of selected clinical features = 5
-
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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.