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 9 clinical features across 422 patients, 24 significant findings detected with P value < 0.05.
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CNMF clustering analysis on array-based mRNA expression data identified 4 subtypes that correlate to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
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Consensus hierarchical clustering analysis on array-based mRNA expression data identified 4 subtypes that correlate to 'HISTOLOGICAL.TYPE'.
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4 subtypes identified in current cancer cohort by 'CN CNMF'. These subtypes correlate to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
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3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'AGE' and 'TUMOR.STAGE'.
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CNMF clustering analysis on RPPA data identified 4 subtypes that correlate to 'HISTOLOGICAL.TYPE'.
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Consensus hierarchical clustering analysis on RPPA data identified 4 subtypes that correlate to 'PATHOLOGICSPREAD(M)'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that correlate to 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'AGE' and 'HISTOLOGICAL.TYPE'.
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CNMF clustering analysis on sequencing-based miR expression data identified 3 subtypes that correlate to 'AGE', 'HISTOLOGICAL.TYPE', and 'PATHOLOGICSPREAD(M)'.
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Consensus hierarchical clustering analysis on sequencing-based miR expression data identified 3 subtypes that correlate to 'AGE' and 'PATHOLOGICSPREAD(M)'.
Clinical Features |
Time to Death |
AGE | GENDER |
HISTOLOGICAL TYPE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
RADIATIONS RADIATION REGIMENINDICATION |
Statistical Tests | logrank test | ANOVA | Fisher's exact test | Fisher's exact test | Chi-square test | Chi-square test | Chi-square test | Chi-square test | Fisher's exact test |
mRNA CNMF subtypes | 0.31 | 0.418 | 0.0625 | 3.12e-06 | 0.89 | 0.0267 | 0.0549 | 0.0374 | |
mRNA cHierClus subtypes | 0.755 | 0.146 | 0.0978 | 3.57e-09 | 0.561 | 0.58 | 0.848 | 0.509 | |
CN CNMF | 0.755 | 0.472 | 0.487 | 3.7e-08 | 0.944 | 0.00113 | 0.00999 | 3.6e-05 | 0.337 |
METHLYATION CNMF | 0.928 | 0.00205 | 0.0531 | 0.0769 | 0.375 | 0.904 | 0.304 | 0.036 | 0.473 |
RPPA CNMF subtypes | 0.429 | 0.501 | 0.306 | 0.015 | 0.23 | 0.141 | 0.186 | 0.117 | 0.302 |
RPPA cHierClus subtypes | 0.302 | 0.169 | 0.348 | 0.464 | 0.28 | 0.123 | 0.0432 | 0.0747 | 0.339 |
RNAseq CNMF subtypes | 0.871 | 0.105 | 0.00324 | 2.4e-07 | 0.7 | 0.0246 | 0.022 | 0.00265 | 1 |
RNAseq cHierClus subtypes | 0.311 | 0.00338 | 0.456 | 8.97e-08 | 0.638 | 0.238 | 0.342 | 0.631 | 1 |
MIRseq CNMF subtypes | 0.246 | 0.000748 | 0.525 | 0.0162 | 0.264 | 0.515 | 1.25e-05 | 0.596 | 0.544 |
MIRseq cHierClus subtypes | 0.521 | 0.00978 | 0.514 | 0.67 | 0.498 | 0.95 | 7.64e-06 | 0.448 | 1 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 63 | 35 | 31 | 26 |
P value = 0.31 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 75 | 11 | 0.9 - 52.0 (5.0) |
subtype1 | 27 | 6 | 1.0 - 41.0 (14.4) |
subtype2 | 22 | 1 | 1.0 - 30.0 (1.0) |
subtype3 | 18 | 3 | 1.0 - 52.0 (8.0) |
subtype4 | 8 | 1 | 0.9 - 1.0 (1.0) |
P value = 0.418 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 155 | 70.6 (11.7) |
subtype1 | 63 | 69.2 (11.9) |
subtype2 | 35 | 72.1 (11.7) |
subtype3 | 31 | 72.7 (10.9) |
subtype4 | 26 | 69.3 (12.1) |
P value = 0.0625 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 76 | 79 |
subtype1 | 32 | 31 |
subtype2 | 23 | 12 |
subtype3 | 11 | 20 |
subtype4 | 10 | 16 |
P value = 3.12e-06 (Fisher's exact test)
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 128 | 24 |
subtype1 | 62 | 1 |
subtype2 | 22 | 12 |
subtype3 | 21 | 9 |
subtype4 | 23 | 2 |
P value = 0.89 (Chi-square test)
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 4 | 31 | 105 | 13 |
subtype1 | 2 | 13 | 43 | 5 |
subtype2 | 1 | 7 | 23 | 2 |
subtype3 | 0 | 6 | 20 | 5 |
subtype4 | 1 | 5 | 19 | 1 |
P value = 0.0267 (Chi-square test)
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 95 | 28 | 32 |
subtype1 | 29 | 15 | 19 |
subtype2 | 24 | 4 | 7 |
subtype3 | 24 | 6 | 1 |
subtype4 | 18 | 3 | 5 |
P value = 0.0549 (Chi-square test)
nPatients | M0 | M1 | M1A |
---|---|---|---|
ALL | 129 | 22 | 1 |
subtype1 | 48 | 15 | 0 |
subtype2 | 30 | 4 | 0 |
subtype3 | 28 | 1 | 1 |
subtype4 | 23 | 2 | 0 |
P value = 0.0374 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 28 | 63 | 39 | 22 |
subtype1 | 12 | 15 | 21 | 15 |
subtype2 | 6 | 17 | 7 | 3 |
subtype3 | 5 | 18 | 5 | 2 |
subtype4 | 5 | 13 | 6 | 2 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 47 | 48 | 14 | 46 |
P value = 0.755 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 75 | 11 | 0.9 - 52.0 (5.0) |
subtype1 | 28 | 2 | 1.0 - 30.0 (1.0) |
subtype2 | 27 | 5 | 1.0 - 41.0 (15.0) |
subtype3 | 7 | 2 | 0.9 - 52.0 (14.4) |
subtype4 | 13 | 2 | 0.9 - 34.0 (1.0) |
P value = 0.146 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 155 | 70.6 (11.7) |
subtype1 | 47 | 73.1 (11.5) |
subtype2 | 48 | 70.7 (9.6) |
subtype3 | 14 | 71.6 (12.8) |
subtype4 | 46 | 67.5 (13.0) |
P value = 0.0978 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 76 | 79 |
subtype1 | 27 | 20 |
subtype2 | 27 | 21 |
subtype3 | 6 | 8 |
subtype4 | 16 | 30 |
P value = 3.57e-09 (Fisher's exact test)
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 128 | 24 |
subtype1 | 25 | 20 |
subtype2 | 46 | 2 |
subtype3 | 12 | 2 |
subtype4 | 45 | 0 |
P value = 0.561 (Chi-square test)
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 4 | 31 | 105 | 13 |
subtype1 | 1 | 10 | 28 | 6 |
subtype2 | 1 | 7 | 36 | 4 |
subtype3 | 1 | 1 | 11 | 1 |
subtype4 | 1 | 13 | 30 | 2 |
P value = 0.58 (Chi-square test)
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 95 | 28 | 32 |
subtype1 | 31 | 7 | 9 |
subtype2 | 25 | 13 | 10 |
subtype3 | 10 | 1 | 3 |
subtype4 | 29 | 7 | 10 |
P value = 0.848 (Chi-square test)
nPatients | M0 | M1 | M1A |
---|---|---|---|
ALL | 129 | 22 | 1 |
subtype1 | 40 | 6 | 0 |
subtype2 | 38 | 8 | 1 |
subtype3 | 12 | 2 | 0 |
subtype4 | 39 | 6 | 0 |
P value = 0.509 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 28 | 63 | 39 | 22 |
subtype1 | 9 | 21 | 10 | 5 |
subtype2 | 5 | 17 | 16 | 9 |
subtype3 | 2 | 8 | 2 | 2 |
subtype4 | 12 | 17 | 11 | 6 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 170 | 187 | 32 | 24 |
P value = 0.755 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 319 | 49 | 0.1 - 135.5 (7.7) |
subtype1 | 127 | 23 | 0.1 - 129.1 (10.0) |
subtype2 | 149 | 19 | 0.1 - 129.1 (6.1) |
subtype3 | 23 | 4 | 0.3 - 135.5 (7.0) |
subtype4 | 20 | 3 | 0.2 - 112.7 (6.0) |
P value = 0.472 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 412 | 67.3 (13.0) |
subtype1 | 170 | 66.4 (12.4) |
subtype2 | 186 | 68.3 (13.7) |
subtype3 | 32 | 66.0 (13.0) |
subtype4 | 24 | 68.2 (12.0) |
P value = 0.487 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 193 | 220 |
subtype1 | 77 | 93 |
subtype2 | 92 | 95 |
subtype3 | 16 | 16 |
subtype4 | 8 | 16 |
P value = 3.7e-08 (Fisher's exact test)
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 356 | 54 |
subtype1 | 162 | 7 |
subtype2 | 140 | 45 |
subtype3 | 31 | 1 |
subtype4 | 23 | 1 |
P value = 0.944 (Chi-square test)
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 11 | 72 | 283 | 45 |
subtype1 | 5 | 27 | 120 | 18 |
subtype2 | 6 | 33 | 124 | 22 |
subtype3 | 0 | 6 | 23 | 3 |
subtype4 | 0 | 6 | 16 | 2 |
P value = 0.00113 (Chi-square test)
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 245 | 95 | 71 |
subtype1 | 78 | 54 | 36 |
subtype2 | 131 | 29 | 27 |
subtype3 | 20 | 7 | 5 |
subtype4 | 16 | 5 | 3 |
P value = 0.00999 (Chi-square test)
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 312 | 49 | 7 | 1 | 36 |
subtype1 | 119 | 32 | 3 | 0 | 14 |
subtype2 | 153 | 10 | 1 | 1 | 18 |
subtype3 | 21 | 6 | 2 | 0 | 2 |
subtype4 | 19 | 1 | 1 | 0 | 2 |
P value = 3.6e-05 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 67 | 157 | 116 | 56 |
subtype1 | 23 | 46 | 60 | 35 |
subtype2 | 35 | 89 | 44 | 11 |
subtype3 | 4 | 13 | 5 | 8 |
subtype4 | 5 | 9 | 7 | 2 |
P value = 0.337 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 3 | 410 |
subtype1 | 3 | 167 |
subtype2 | 0 | 187 |
subtype3 | 0 | 32 |
subtype4 | 0 | 24 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 106 | 86 | 63 |
P value = 0.928 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 237 | 36 | 0.1 - 135.5 (7.6) |
subtype1 | 95 | 15 | 0.1 - 135.5 (8.0) |
subtype2 | 81 | 13 | 0.1 - 129.1 (8.0) |
subtype3 | 61 | 8 | 0.1 - 102.4 (5.8) |
P value = 0.00205 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 254 | 65.4 (13.3) |
subtype1 | 106 | 66.3 (13.1) |
subtype2 | 86 | 68.0 (13.1) |
subtype3 | 62 | 60.5 (12.6) |
P value = 0.0531 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 115 | 140 |
subtype1 | 42 | 64 |
subtype2 | 48 | 38 |
subtype3 | 25 | 38 |
P value = 0.0769 (Fisher's exact test)
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 225 | 30 |
subtype1 | 99 | 7 |
subtype2 | 73 | 13 |
subtype3 | 53 | 10 |
P value = 0.375 (Chi-square test)
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 7 | 38 | 178 | 31 |
subtype1 | 3 | 18 | 72 | 13 |
subtype2 | 3 | 16 | 58 | 8 |
subtype3 | 1 | 4 | 48 | 10 |
P value = 0.904 (Chi-square test)
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 152 | 64 | 37 |
subtype1 | 59 | 29 | 16 |
subtype2 | 53 | 20 | 13 |
subtype3 | 40 | 15 | 8 |
P value = 0.304 (Chi-square test)
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 180 | 27 | 6 | 1 | 36 |
subtype1 | 69 | 16 | 4 | 0 | 16 |
subtype2 | 61 | 6 | 1 | 1 | 14 |
subtype3 | 50 | 5 | 1 | 0 | 6 |
P value = 0.036 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 37 | 98 | 72 | 34 |
subtype1 | 15 | 34 | 31 | 20 |
subtype2 | 18 | 32 | 23 | 9 |
subtype3 | 4 | 32 | 18 | 5 |
P value = 0.473 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 3 | 252 |
subtype1 | 2 | 104 |
subtype2 | 0 | 86 |
subtype3 | 1 | 62 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 65 | 119 | 7 | 78 |
P value = 0.429 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 206 | 19 | 0.1 - 105.3 (6.0) |
subtype1 | 56 | 2 | 0.1 - 87.8 (5.2) |
subtype2 | 82 | 7 | 0.1 - 75.2 (6.5) |
subtype3 | 2 | 0 | 0.6 - 18.1 (9.4) |
subtype4 | 66 | 10 | 0.1 - 105.3 (6.0) |
P value = 0.501 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 268 | 66.6 (13.3) |
subtype1 | 65 | 66.7 (12.0) |
subtype2 | 118 | 66.2 (13.4) |
subtype3 | 7 | 74.1 (9.4) |
subtype4 | 78 | 66.3 (14.6) |
P value = 0.306 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 127 | 142 |
subtype1 | 34 | 31 |
subtype2 | 55 | 64 |
subtype3 | 1 | 6 |
subtype4 | 37 | 41 |
P value = 0.015 (Fisher's exact test)
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 238 | 30 |
subtype1 | 51 | 14 |
subtype2 | 112 | 7 |
subtype3 | 6 | 1 |
subtype4 | 69 | 8 |
P value = 0.23 (Chi-square test)
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 5 | 45 | 185 | 31 |
subtype1 | 0 | 9 | 46 | 10 |
subtype2 | 1 | 22 | 82 | 11 |
subtype3 | 0 | 0 | 7 | 0 |
subtype4 | 4 | 14 | 50 | 10 |
P value = 0.141 (Chi-square test)
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 160 | 66 | 42 |
subtype1 | 33 | 19 | 12 |
subtype2 | 66 | 31 | 22 |
subtype3 | 6 | 0 | 1 |
subtype4 | 55 | 16 | 7 |
P value = 0.186 (Chi-square test)
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 202 | 31 | 6 | 1 | 26 |
subtype1 | 50 | 7 | 3 | 0 | 4 |
subtype2 | 84 | 20 | 0 | 1 | 13 |
subtype3 | 7 | 0 | 0 | 0 | 0 |
subtype4 | 61 | 4 | 3 | 0 | 9 |
P value = 0.117 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 40 | 107 | 77 | 38 |
subtype1 | 7 | 24 | 22 | 10 |
subtype2 | 19 | 39 | 35 | 21 |
subtype3 | 0 | 6 | 1 | 0 |
subtype4 | 14 | 38 | 19 | 7 |
P value = 0.302 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 3 | 266 |
subtype1 | 2 | 63 |
subtype2 | 1 | 118 |
subtype3 | 0 | 7 |
subtype4 | 0 | 78 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 143 | 25 | 49 | 52 |
P value = 0.302 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 206 | 19 | 0.1 - 105.3 (6.0) |
subtype1 | 100 | 11 | 0.1 - 103.0 (6.6) |
subtype2 | 15 | 1 | 0.1 - 105.3 (8.0) |
subtype3 | 44 | 6 | 0.1 - 100.0 (5.1) |
subtype4 | 47 | 1 | 0.1 - 87.8 (5.4) |
P value = 0.169 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 268 | 66.6 (13.3) |
subtype1 | 142 | 68.0 (13.6) |
subtype2 | 25 | 67.9 (12.0) |
subtype3 | 49 | 63.9 (13.8) |
subtype4 | 52 | 64.6 (12.6) |
P value = 0.348 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 127 | 142 |
subtype1 | 71 | 72 |
subtype2 | 14 | 11 |
subtype3 | 18 | 31 |
subtype4 | 24 | 28 |
P value = 0.464 (Fisher's exact test)
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 238 | 30 |
subtype1 | 129 | 13 |
subtype2 | 23 | 2 |
subtype3 | 41 | 8 |
subtype4 | 45 | 7 |
P value = 0.28 (Chi-square test)
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 5 | 45 | 185 | 31 |
subtype1 | 1 | 23 | 99 | 17 |
subtype2 | 0 | 3 | 20 | 2 |
subtype3 | 3 | 12 | 30 | 4 |
subtype4 | 1 | 7 | 36 | 8 |
P value = 0.123 (Chi-square test)
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 160 | 66 | 42 |
subtype1 | 78 | 39 | 26 |
subtype2 | 19 | 5 | 1 |
subtype3 | 36 | 8 | 5 |
subtype4 | 27 | 14 | 10 |
P value = 0.0432 (Chi-square test)
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 202 | 31 | 6 | 1 | 26 |
subtype1 | 103 | 22 | 0 | 1 | 17 |
subtype2 | 22 | 0 | 0 | 0 | 1 |
subtype3 | 39 | 2 | 3 | 0 | 5 |
subtype4 | 38 | 7 | 3 | 0 | 3 |
P value = 0.0747 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 40 | 107 | 77 | 38 |
subtype1 | 20 | 51 | 45 | 23 |
subtype2 | 2 | 16 | 6 | 0 |
subtype3 | 11 | 23 | 10 | 5 |
subtype4 | 7 | 17 | 16 | 10 |
P value = 0.339 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 3 | 266 |
subtype1 | 1 | 142 |
subtype2 | 0 | 25 |
subtype3 | 0 | 49 |
subtype4 | 2 | 50 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 68 | 61 | 40 | 23 |
P value = 0.871 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 108 | 16 | 0.9 - 71.7 (12.4) |
subtype1 | 36 | 6 | 0.9 - 71.7 (15.9) |
subtype2 | 41 | 5 | 1.0 - 49.0 (8.1) |
subtype3 | 25 | 5 | 0.9 - 52.0 (12.0) |
subtype4 | 6 | 0 | 1.0 - 4.0 (1.0) |
P value = 0.105 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 192 | 69.7 (12.4) |
subtype1 | 68 | 66.8 (13.0) |
subtype2 | 61 | 72.0 (12.2) |
subtype3 | 40 | 70.6 (10.9) |
subtype4 | 23 | 70.1 (12.9) |
P value = 0.00324 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 99 | 93 |
subtype1 | 38 | 30 |
subtype2 | 40 | 21 |
subtype3 | 13 | 27 |
subtype4 | 8 | 15 |
P value = 2.4e-07 (Fisher's exact test)
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 162 | 27 |
subtype1 | 67 | 0 |
subtype2 | 41 | 19 |
subtype3 | 32 | 7 |
subtype4 | 22 | 1 |
P value = 0.7 (Chi-square test)
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 6 | 38 | 128 | 18 |
subtype1 | 2 | 15 | 44 | 7 |
subtype2 | 2 | 8 | 41 | 8 |
subtype3 | 1 | 8 | 28 | 3 |
subtype4 | 1 | 7 | 15 | 0 |
P value = 0.0246 (Chi-square test)
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 114 | 41 | 36 |
subtype1 | 31 | 20 | 16 |
subtype2 | 34 | 15 | 12 |
subtype3 | 31 | 4 | 5 |
subtype4 | 18 | 2 | 3 |
P value = 0.022 (Chi-square test)
nPatients | M0 | M1 | M1A |
---|---|---|---|
ALL | 159 | 28 | 2 |
subtype1 | 47 | 18 | 1 |
subtype2 | 53 | 7 | 1 |
subtype3 | 37 | 2 | 0 |
subtype4 | 22 | 1 | 0 |
P value = 0.00265 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 35 | 73 | 50 | 27 |
subtype1 | 11 | 16 | 21 | 17 |
subtype2 | 8 | 25 | 19 | 7 |
subtype3 | 8 | 22 | 6 | 2 |
subtype4 | 8 | 10 | 4 | 1 |
P value = 1 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 1 | 191 |
subtype1 | 1 | 67 |
subtype2 | 0 | 61 |
subtype3 | 0 | 40 |
subtype4 | 0 | 23 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 67 | 19 | 106 |
P value = 0.311 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 108 | 16 | 0.9 - 71.7 (12.4) |
subtype1 | 44 | 8 | 1.0 - 52.0 (8.0) |
subtype2 | 11 | 0 | 7.0 - 34.0 (15.2) |
subtype3 | 53 | 8 | 0.9 - 71.7 (10.9) |
P value = 0.00338 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 192 | 69.7 (12.4) |
subtype1 | 67 | 73.4 (11.6) |
subtype2 | 19 | 71.1 (12.6) |
subtype3 | 106 | 67.0 (12.4) |
P value = 0.456 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 99 | 93 |
subtype1 | 36 | 31 |
subtype2 | 12 | 7 |
subtype3 | 51 | 55 |
P value = 8.97e-08 (Fisher's exact test)
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 162 | 27 |
subtype1 | 43 | 22 |
subtype2 | 17 | 2 |
subtype3 | 102 | 3 |
P value = 0.638 (Chi-square test)
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 6 | 38 | 128 | 18 |
subtype1 | 2 | 14 | 41 | 8 |
subtype2 | 0 | 2 | 14 | 3 |
subtype3 | 4 | 22 | 73 | 7 |
P value = 0.238 (Chi-square test)
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 114 | 41 | 36 |
subtype1 | 44 | 15 | 8 |
subtype2 | 10 | 2 | 6 |
subtype3 | 60 | 24 | 22 |
P value = 0.342 (Chi-square test)
nPatients | M0 | M1 | M1A |
---|---|---|---|
ALL | 159 | 28 | 2 |
subtype1 | 59 | 6 | 1 |
subtype2 | 13 | 5 | 0 |
subtype3 | 87 | 17 | 1 |
P value = 0.631 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 35 | 73 | 50 | 27 |
subtype1 | 14 | 29 | 16 | 6 |
subtype2 | 2 | 7 | 4 | 4 |
subtype3 | 19 | 37 | 30 | 17 |
P value = 1 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 1 | 191 |
subtype1 | 0 | 67 |
subtype2 | 0 | 19 |
subtype3 | 1 | 105 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 182 | 163 | 62 |
P value = 0.246 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 309 | 49 | 0.1 - 135.5 (7.5) |
subtype1 | 98 | 17 | 0.9 - 71.7 (7.3) |
subtype2 | 153 | 26 | 0.1 - 135.5 (9.4) |
subtype3 | 58 | 6 | 0.1 - 100.0 (4.3) |
P value = 0.000748 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 406 | 67.3 (13.1) |
subtype1 | 182 | 69.8 (12.5) |
subtype2 | 162 | 66.0 (12.6) |
subtype3 | 62 | 63.3 (14.8) |
P value = 0.525 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 192 | 215 |
subtype1 | 91 | 91 |
subtype2 | 75 | 88 |
subtype3 | 26 | 36 |
P value = 0.0162 (Fisher's exact test)
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 349 | 55 |
subtype1 | 154 | 25 |
subtype2 | 148 | 15 |
subtype3 | 47 | 15 |
P value = 0.264 (Chi-square test)
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 11 | 69 | 279 | 45 |
subtype1 | 6 | 37 | 120 | 17 |
subtype2 | 5 | 23 | 117 | 17 |
subtype3 | 0 | 9 | 42 | 11 |
P value = 0.515 (Chi-square test)
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 241 | 94 | 70 |
subtype1 | 111 | 36 | 34 |
subtype2 | 98 | 40 | 25 |
subtype3 | 32 | 18 | 11 |
P value = 1.25e-05 (Chi-square test)
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 305 | 50 | 7 | 1 | 36 |
subtype1 | 148 | 28 | 1 | 0 | 1 |
subtype2 | 111 | 15 | 5 | 1 | 28 |
subtype3 | 46 | 7 | 1 | 0 | 7 |
P value = 0.596 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 65 | 155 | 113 | 57 |
subtype1 | 34 | 69 | 45 | 27 |
subtype2 | 26 | 63 | 48 | 22 |
subtype3 | 5 | 23 | 20 | 8 |
P value = 0.544 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 3 | 404 |
subtype1 | 1 | 181 |
subtype2 | 1 | 162 |
subtype3 | 1 | 61 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 180 | 45 | 182 |
P value = 0.521 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 309 | 49 | 0.1 - 135.5 (7.5) |
subtype1 | 97 | 16 | 0.9 - 71.7 (9.1) |
subtype2 | 42 | 8 | 0.1 - 129.1 (6.7) |
subtype3 | 170 | 25 | 0.1 - 135.5 (7.0) |
P value = 0.00978 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 406 | 67.3 (13.1) |
subtype1 | 180 | 69.5 (12.6) |
subtype2 | 45 | 66.4 (11.8) |
subtype3 | 181 | 65.3 (13.6) |
P value = 0.514 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 192 | 215 |
subtype1 | 90 | 90 |
subtype2 | 22 | 23 |
subtype3 | 80 | 102 |
P value = 0.67 (Fisher's exact test)
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 349 | 55 |
subtype1 | 151 | 26 |
subtype2 | 41 | 4 |
subtype3 | 157 | 25 |
P value = 0.498 (Chi-square test)
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 11 | 69 | 279 | 45 |
subtype1 | 6 | 36 | 119 | 17 |
subtype2 | 2 | 5 | 30 | 7 |
subtype3 | 3 | 28 | 130 | 21 |
P value = 0.95 (Chi-square test)
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 241 | 94 | 70 |
subtype1 | 107 | 39 | 33 |
subtype2 | 27 | 10 | 8 |
subtype3 | 107 | 45 | 29 |
P value = 7.64e-06 (Chi-square test)
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 305 | 50 | 7 | 1 | 36 |
subtype1 | 145 | 29 | 2 | 0 | 0 |
subtype2 | 30 | 5 | 2 | 0 | 6 |
subtype3 | 130 | 16 | 3 | 1 | 30 |
P value = 0.448 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 65 | 155 | 113 | 57 |
subtype1 | 34 | 64 | 45 | 28 |
subtype2 | 8 | 18 | 10 | 7 |
subtype3 | 23 | 73 | 58 | 22 |
P value = 1 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 3 | 404 |
subtype1 | 1 | 179 |
subtype2 | 0 | 45 |
subtype3 | 2 | 180 |
-
Cluster data file = COAD-TP.mergedcluster.txt
-
Clinical data file = COAD-TP.clin.merged.picked.txt
-
Number of patients = 422
-
Number of clustering approaches = 10
-
Number of selected clinical features = 9
-
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 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 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
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.