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 10 clinical features across 422 patients, 27 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', 'GENDER', 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', 'PATHOLOGICSPREAD(M)', and 'NEOADJUVANT.THERAPY'.
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Consensus hierarchical clustering analysis on sequencing-based miR expression data identified 3 subtypes that correlate to 'AGE', 'PATHOLOGICSPREAD(M)', and 'NEOADJUVANT.THERAPY'.
Clinical Features |
Time to Death |
AGE | GENDER |
HISTOLOGICAL TYPE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
RADIATIONS RADIATION REGIMENINDICATION |
NEOADJUVANT THERAPY |
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 | Fisher's exact test |
mRNA CNMF subtypes | 0.0584 | 0.418 | 0.0625 | 3.12e-06 | 0.89 | 0.0267 | 0.0549 | 0.0374 | 0.266 | |
mRNA cHierClus subtypes | 0.275 | 0.146 | 0.0978 | 3.57e-09 | 0.561 | 0.58 | 0.848 | 0.509 | 0.732 | |
CN CNMF | 0.275 | 0.472 | 0.487 | 3.7e-08 | 0.944 | 0.00113 | 0.00999 | 3.6e-05 | 0.337 | 0.391 |
METHLYATION CNMF | 0.687 | 0.00205 | 0.0362 | 0.0734 | 0.374 | 0.926 | 0.321 | 0.039 | 0.474 | 0.92 |
RPPA CNMF subtypes | 0.193 | 0.501 | 0.306 | 0.015 | 0.23 | 0.141 | 0.186 | 0.117 | 0.302 | 0.172 |
RPPA cHierClus subtypes | 0.0562 | 0.169 | 0.348 | 0.464 | 0.28 | 0.123 | 0.0432 | 0.0747 | 0.339 | 0.387 |
RNAseq CNMF subtypes | 0.399 | 0.105 | 0.00324 | 2.4e-07 | 0.7 | 0.0246 | 0.022 | 0.00265 | 1 | 0.337 |
RNAseq cHierClus subtypes | 0.127 | 0.00338 | 0.456 | 8.97e-08 | 0.638 | 0.238 | 0.342 | 0.631 | 1 | 0.381 |
MIRseq CNMF subtypes | 0.0939 | 0.000748 | 0.525 | 0.0162 | 0.264 | 0.515 | 1.25e-05 | 0.596 | 0.544 | 0.000559 |
MIRseq cHierClus subtypes | 0.253 | 0.00978 | 0.514 | 0.67 | 0.498 | 0.95 | 7.64e-06 | 0.448 | 1 | 0.00584 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 63 | 35 | 31 | 26 |
P value = 0.0584 (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 = 0.275 (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 = 0.275 (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 |
P value = 0.391 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 58 | 355 |
subtype1 | 28 | 142 |
subtype2 | 26 | 161 |
subtype3 | 3 | 29 |
subtype4 | 1 | 23 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 107 | 85 | 63 |
P value = 0.687 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 237 | 36 | 0.1 - 135.5 (7.6) |
subtype1 | 96 | 15 | 0.1 - 135.5 (8.0) |
subtype2 | 80 | 13 | 0.1 - 129.1 (8.1) |
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 | 107 | 66.3 (13.1) |
subtype2 | 85 | 68.0 (13.2) |
subtype3 | 62 | 60.5 (12.6) |
P value = 0.0362 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 115 | 140 |
subtype1 | 42 | 65 |
subtype2 | 48 | 37 |
subtype3 | 25 | 38 |
P value = 0.0734 (Fisher's exact test)
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 225 | 30 |
subtype1 | 100 | 7 |
subtype2 | 72 | 13 |
subtype3 | 53 | 10 |
P value = 0.374 (Chi-square test)
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 7 | 38 | 178 | 31 |
subtype1 | 3 | 18 | 73 | 13 |
subtype2 | 3 | 16 | 57 | 8 |
subtype3 | 1 | 4 | 48 | 10 |
P value = 0.926 (Chi-square test)
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 152 | 64 | 37 |
subtype1 | 60 | 29 | 16 |
subtype2 | 52 | 20 | 13 |
subtype3 | 40 | 15 | 8 |
P value = 0.321 (Chi-square test)
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 180 | 27 | 6 | 1 | 36 |
subtype1 | 70 | 16 | 4 | 0 | 16 |
subtype2 | 60 | 6 | 1 | 1 | 14 |
subtype3 | 50 | 5 | 1 | 0 | 6 |
P value = 0.039 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 37 | 98 | 72 | 34 |
subtype1 | 15 | 35 | 31 | 20 |
subtype2 | 18 | 31 | 23 | 9 |
subtype3 | 4 | 32 | 18 | 5 |
P value = 0.474 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 3 | 252 |
subtype1 | 2 | 105 |
subtype2 | 0 | 85 |
subtype3 | 1 | 62 |
P value = 0.92 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 51 | 204 |
subtype1 | 20 | 87 |
subtype2 | 18 | 67 |
subtype3 | 13 | 50 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 65 | 119 | 7 | 78 |
P value = 0.193 (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 |
P value = 0.172 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 51 | 218 |
subtype1 | 18 | 47 |
subtype2 | 20 | 99 |
subtype3 | 0 | 7 |
subtype4 | 13 | 65 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 143 | 25 | 49 | 52 |
P value = 0.0562 (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 |
P value = 0.387 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 51 | 218 |
subtype1 | 23 | 120 |
subtype2 | 5 | 20 |
subtype3 | 9 | 40 |
subtype4 | 14 | 38 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 68 | 61 | 40 | 23 |
P value = 0.399 (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 |
P value = 0.337 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 15 | 177 |
subtype1 | 8 | 60 |
subtype2 | 5 | 56 |
subtype3 | 2 | 38 |
subtype4 | 0 | 23 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 67 | 19 | 106 |
P value = 0.127 (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 |
P value = 0.381 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 15 | 177 |
subtype1 | 3 | 64 |
subtype2 | 1 | 18 |
subtype3 | 11 | 95 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 182 | 163 | 62 |
P value = 0.0939 (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 |
P value = 0.000559 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 58 | 349 |
subtype1 | 13 | 169 |
subtype2 | 34 | 129 |
subtype3 | 11 | 51 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 180 | 45 | 182 |
P value = 0.253 (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 |
P value = 0.00584 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 58 | 349 |
subtype1 | 15 | 165 |
subtype2 | 10 | 35 |
subtype3 | 33 | 149 |
-
Cluster data file = COAD.mergedcluster.txt
-
Clinical data file = COAD.clin.merged.picked.txt
-
Number of patients = 422
-
Number of clustering approaches = 10
-
Number of selected clinical features = 10
-
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.