(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 9 clinical features across 166 patients, 3 significant findings detected with P value < 0.05 and Q value < 0.25.
-
CNMF clustering analysis on array-based mRNA expression data identified 3 subtypes that do not correlate to any clinical features.
-
Consensus hierarchical clustering analysis on array-based mRNA expression data identified 3 subtypes that do not correlate to any clinical features.
-
5 subtypes identified in current cancer cohort by 'CN CNMF'. These subtypes do not correlate to any clinical features.
-
3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes do not correlate to any clinical features.
-
CNMF clustering analysis on RPPA data identified 3 subtypes that do not correlate to any clinical features.
-
Consensus hierarchical clustering analysis on RPPA data identified 5 subtypes that do not correlate to any clinical features.
-
CNMF clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that correlate to 'HISTOLOGICAL.TYPE'.
-
Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'HISTOLOGICAL.TYPE'.
-
CNMF clustering analysis on sequencing-based miR expression data identified 5 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on sequencing-based miR expression data identified 3 subtypes that correlate to '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 |
0.274 (1.00) |
0.499 (1.00) |
0.953 (1.00) |
0.365 (1.00) |
0.0987 (1.00) |
0.66 (1.00) |
0.407 (1.00) |
0.639 (1.00) |
0.29 (1.00) |
mRNA cHierClus subtypes |
0.0075 (0.639) |
0.394 (1.00) |
0.865 (1.00) |
0.692 (1.00) |
0.245 (1.00) |
0.574 (1.00) |
0.212 (1.00) |
0.504 (1.00) |
1 (1.00) |
CN CNMF |
0.00743 (0.639) |
0.373 (1.00) |
0.568 (1.00) |
0.0316 (1.00) |
0.564 (1.00) |
0.104 (1.00) |
0.0929 (1.00) |
0.477 (1.00) |
0.238 (1.00) |
METHLYATION CNMF |
0.58 (1.00) |
0.291 (1.00) |
0.494 (1.00) |
0.274 (1.00) |
0.524 (1.00) |
0.708 (1.00) |
0.261 (1.00) |
0.0317 (1.00) |
0.857 (1.00) |
RPPA CNMF subtypes |
0.904 (1.00) |
0.513 (1.00) |
0.0423 (1.00) |
0.255 (1.00) |
0.2 (1.00) |
0.114 (1.00) |
0.0137 (1.00) |
0.157 (1.00) |
1 (1.00) |
RPPA cHierClus subtypes |
0.0032 (0.278) |
0.0282 (1.00) |
0.378 (1.00) |
0.157 (1.00) |
0.402 (1.00) |
0.0918 (1.00) |
0.0124 (1.00) |
0.218 (1.00) |
0.785 (1.00) |
RNAseq CNMF subtypes |
0.66 (1.00) |
0.478 (1.00) |
0.586 (1.00) |
0.00271 (0.238) |
0.143 (1.00) |
0.702 (1.00) |
0.696 (1.00) |
0.562 (1.00) |
0.472 (1.00) |
RNAseq cHierClus subtypes |
0.382 (1.00) |
0.283 (1.00) |
0.87 (1.00) |
2.93e-05 (0.00263) |
0.709 (1.00) |
0.761 (1.00) |
0.589 (1.00) |
0.842 (1.00) |
0.569 (1.00) |
MIRseq CNMF subtypes |
0.314 (1.00) |
0.892 (1.00) |
0.461 (1.00) |
0.313 (1.00) |
0.251 (1.00) |
0.0172 (1.00) |
0.0461 (1.00) |
0.117 (1.00) |
0.283 (1.00) |
MIRseq cHierClus subtypes |
0.774 (1.00) |
0.582 (1.00) |
0.973 (1.00) |
0.037 (1.00) |
0.726 (1.00) |
0.244 (1.00) |
0.000442 (0.0394) |
0.361 (1.00) |
0.298 (1.00) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 25 | 20 | 24 |
P value = 0.274 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 39 | 4 | 0.9 - 52.0 (6.0) |
subtype1 | 20 | 1 | 0.9 - 49.9 (13.3) |
subtype2 | 7 | 0 | 1.0 - 12.7 (1.0) |
subtype3 | 12 | 3 | 1.0 - 52.0 (1.5) |
P value = 0.499 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 69 | 66.6 (10.7) |
subtype1 | 25 | 64.6 (12.3) |
subtype2 | 20 | 67.9 (9.9) |
subtype3 | 24 | 67.7 (9.5) |
P value = 0.953 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 31 | 38 |
subtype1 | 12 | 13 |
subtype2 | 9 | 11 |
subtype3 | 10 | 14 |
P value = 0.365 (Fisher's exact test), Q value = 1
nPatients | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 58 | 7 |
subtype1 | 19 | 3 |
subtype2 | 16 | 3 |
subtype3 | 23 | 1 |
P value = 0.0987 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 5 | 15 | 45 | 4 |
subtype1 | 3 | 6 | 16 | 0 |
subtype2 | 2 | 5 | 13 | 0 |
subtype3 | 0 | 4 | 16 | 4 |
P value = 0.66 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 42 | 15 | 12 |
subtype1 | 16 | 5 | 4 |
subtype2 | 14 | 4 | 2 |
subtype3 | 12 | 6 | 6 |
P value = 0.407 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 |
---|---|---|
ALL | 57 | 12 |
subtype1 | 21 | 4 |
subtype2 | 18 | 2 |
subtype3 | 18 | 6 |
P value = 0.639 (Chi-square test), Q value = 1
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 18 | 23 | 16 | 10 |
subtype1 | 8 | 8 | 5 | 3 |
subtype2 | 7 | 7 | 4 | 2 |
subtype3 | 3 | 8 | 7 | 5 |
P value = 0.29 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 1 | 68 |
subtype1 | 0 | 25 |
subtype2 | 1 | 19 |
subtype3 | 0 | 24 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 19 | 24 | 26 |
P value = 0.0075 (logrank test), Q value = 0.64
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 39 | 4 | 0.9 - 52.0 (6.0) |
subtype1 | 10 | 2 | 1.0 - 38.0 (1.0) |
subtype2 | 20 | 2 | 0.9 - 52.0 (13.7) |
subtype3 | 9 | 0 | 1.0 - 17.0 (1.0) |
P value = 0.394 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 69 | 66.6 (10.7) |
subtype1 | 19 | 68.4 (8.7) |
subtype2 | 24 | 64.2 (12.8) |
subtype3 | 26 | 67.5 (9.7) |
P value = 0.865 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 31 | 38 |
subtype1 | 8 | 11 |
subtype2 | 12 | 12 |
subtype3 | 11 | 15 |
P value = 0.692 (Fisher's exact test), Q value = 1
nPatients | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 58 | 7 |
subtype1 | 18 | 1 |
subtype2 | 19 | 3 |
subtype3 | 21 | 3 |
P value = 0.245 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 5 | 15 | 45 | 4 |
subtype1 | 0 | 3 | 13 | 3 |
subtype2 | 3 | 6 | 14 | 1 |
subtype3 | 2 | 6 | 18 | 0 |
P value = 0.574 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 42 | 15 | 12 |
subtype1 | 9 | 6 | 4 |
subtype2 | 15 | 4 | 5 |
subtype3 | 18 | 5 | 3 |
P value = 0.212 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 |
---|---|---|
ALL | 57 | 12 |
subtype1 | 14 | 5 |
subtype2 | 19 | 5 |
subtype3 | 24 | 2 |
P value = 0.504 (Chi-square test), Q value = 1
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 18 | 23 | 16 | 10 |
subtype1 | 2 | 6 | 6 | 4 |
subtype2 | 8 | 7 | 4 | 4 |
subtype3 | 8 | 10 | 6 | 2 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 1 | 68 |
subtype1 | 0 | 19 |
subtype2 | 0 | 24 |
subtype3 | 1 | 25 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 7 | 32 | 46 | 55 | 22 |
P value = 0.00743 (logrank test), Q value = 0.64
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 125 | 11 | 0.2 - 121.1 (6.3) |
subtype1 | 7 | 0 | 0.4 - 121.1 (9.4) |
subtype2 | 24 | 4 | 1.0 - 51.5 (5.0) |
subtype3 | 31 | 3 | 0.5 - 119.5 (6.3) |
subtype4 | 46 | 1 | 0.2 - 70.0 (4.7) |
subtype5 | 17 | 3 | 0.8 - 38.9 (13.0) |
P value = 0.373 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 162 | 64.7 (11.8) |
subtype1 | 7 | 61.9 (9.9) |
subtype2 | 32 | 64.4 (11.8) |
subtype3 | 46 | 66.4 (12.5) |
subtype4 | 55 | 62.7 (11.9) |
subtype5 | 22 | 67.5 (10.3) |
P value = 0.568 (Chi-square test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 74 | 88 |
subtype1 | 1 | 6 |
subtype2 | 15 | 17 |
subtype3 | 22 | 24 |
subtype4 | 26 | 29 |
subtype5 | 10 | 12 |
P value = 0.0316 (Chi-square test), Q value = 1
nPatients | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 143 | 13 |
subtype1 | 7 | 0 |
subtype2 | 32 | 0 |
subtype3 | 40 | 4 |
subtype4 | 44 | 9 |
subtype5 | 20 | 0 |
P value = 0.564 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 9 | 29 | 109 | 14 |
subtype1 | 1 | 0 | 5 | 1 |
subtype2 | 1 | 4 | 23 | 3 |
subtype3 | 1 | 8 | 31 | 6 |
subtype4 | 5 | 14 | 34 | 2 |
subtype5 | 1 | 3 | 16 | 2 |
P value = 0.104 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 83 | 45 | 32 |
subtype1 | 5 | 0 | 2 |
subtype2 | 14 | 12 | 5 |
subtype3 | 23 | 11 | 11 |
subtype4 | 34 | 15 | 6 |
subtype5 | 7 | 7 | 8 |
P value = 0.0929 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1A | MX |
---|---|---|---|---|
ALL | 123 | 22 | 2 | 13 |
subtype1 | 7 | 0 | 0 | 0 |
subtype2 | 22 | 9 | 0 | 0 |
subtype3 | 34 | 7 | 0 | 5 |
subtype4 | 45 | 4 | 1 | 4 |
subtype5 | 15 | 2 | 1 | 4 |
P value = 0.477 (Chi-square test), Q value = 1
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 30 | 50 | 50 | 25 |
subtype1 | 1 | 4 | 2 | 0 |
subtype2 | 4 | 9 | 9 | 7 |
subtype3 | 6 | 17 | 13 | 7 |
subtype4 | 16 | 15 | 16 | 7 |
subtype5 | 3 | 5 | 10 | 4 |
P value = 0.238 (Chi-square test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 6 | 156 |
subtype1 | 1 | 6 |
subtype2 | 0 | 32 |
subtype3 | 1 | 45 |
subtype4 | 2 | 53 |
subtype5 | 2 | 20 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 27 | 38 | 30 |
P value = 0.58 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 88 | 8 | 0.2 - 121.1 (6.2) |
subtype1 | 27 | 2 | 0.2 - 121.1 (6.9) |
subtype2 | 35 | 3 | 0.2 - 60.0 (7.4) |
subtype3 | 26 | 3 | 0.3 - 72.1 (3.0) |
P value = 0.291 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 95 | 63.3 (12.3) |
subtype1 | 27 | 60.3 (9.4) |
subtype2 | 38 | 63.9 (12.8) |
subtype3 | 30 | 65.3 (13.6) |
P value = 0.494 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 42 | 53 |
subtype1 | 11 | 16 |
subtype2 | 15 | 23 |
subtype3 | 16 | 14 |
P value = 0.274 (Fisher's exact test), Q value = 1
nPatients | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 87 | 6 |
subtype1 | 26 | 1 |
subtype2 | 35 | 1 |
subtype3 | 26 | 4 |
P value = 0.524 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 4 | 13 | 66 | 11 |
subtype1 | 2 | 4 | 18 | 3 |
subtype2 | 1 | 7 | 23 | 6 |
subtype3 | 1 | 2 | 25 | 2 |
P value = 0.708 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 41 | 30 | 21 |
subtype1 | 12 | 8 | 6 |
subtype2 | 14 | 15 | 8 |
subtype3 | 15 | 7 | 7 |
P value = 0.261 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1A | MX |
---|---|---|---|---|
ALL | 67 | 10 | 2 | 14 |
subtype1 | 17 | 6 | 1 | 3 |
subtype2 | 27 | 1 | 1 | 7 |
subtype3 | 23 | 3 | 0 | 4 |
P value = 0.0317 (Chi-square test), Q value = 1
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 11 | 28 | 35 | 15 |
subtype1 | 5 | 7 | 7 | 7 |
subtype2 | 5 | 7 | 19 | 3 |
subtype3 | 1 | 14 | 9 | 5 |
P value = 0.857 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 5 | 90 |
subtype1 | 2 | 25 |
subtype2 | 2 | 36 |
subtype3 | 1 | 29 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 54 | 34 | 42 |
P value = 0.904 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 102 | 11 | 0.2 - 121.1 (6.2) |
subtype1 | 40 | 5 | 0.2 - 121.1 (5.6) |
subtype2 | 24 | 2 | 0.3 - 72.1 (3.6) |
subtype3 | 38 | 4 | 0.2 - 70.0 (8.1) |
P value = 0.513 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 130 | 65.6 (11.7) |
subtype1 | 54 | 64.8 (12.3) |
subtype2 | 34 | 67.6 (11.5) |
subtype3 | 42 | 64.9 (11.2) |
P value = 0.0423 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 60 | 70 |
subtype1 | 32 | 22 |
subtype2 | 12 | 22 |
subtype3 | 16 | 26 |
P value = 0.255 (Fisher's exact test), Q value = 1
nPatients | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 117 | 10 |
subtype1 | 48 | 5 |
subtype2 | 28 | 4 |
subtype3 | 41 | 1 |
P value = 0.2 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 5 | 23 | 91 | 10 |
subtype1 | 4 | 10 | 36 | 4 |
subtype2 | 1 | 4 | 23 | 5 |
subtype3 | 0 | 9 | 32 | 1 |
P value = 0.114 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 64 | 37 | 26 |
subtype1 | 24 | 19 | 10 |
subtype2 | 13 | 10 | 10 |
subtype3 | 27 | 8 | 6 |
P value = 0.0137 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1A | MX |
---|---|---|---|---|
ALL | 98 | 18 | 2 | 10 |
subtype1 | 39 | 10 | 0 | 5 |
subtype2 | 24 | 7 | 2 | 0 |
subtype3 | 35 | 1 | 0 | 5 |
P value = 0.157 (Chi-square test), Q value = 1
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 21 | 40 | 42 | 19 |
subtype1 | 9 | 14 | 18 | 10 |
subtype2 | 4 | 9 | 10 | 8 |
subtype3 | 8 | 17 | 14 | 1 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 5 | 125 |
subtype1 | 2 | 52 |
subtype2 | 1 | 33 |
subtype3 | 2 | 40 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 6 | 26 | 20 | 42 | 36 |
P value = 0.0032 (logrank test), Q value = 0.28
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 102 | 11 | 0.2 - 121.1 (6.2) |
subtype1 | 4 | 1 | 0.5 - 24.1 (5.2) |
subtype2 | 11 | 1 | 0.9 - 15.8 (1.0) |
subtype3 | 18 | 1 | 0.3 - 72.1 (5.5) |
subtype4 | 38 | 6 | 0.2 - 119.5 (6.6) |
subtype5 | 31 | 2 | 0.2 - 121.1 (8.0) |
P value = 0.0282 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 130 | 65.6 (11.7) |
subtype1 | 6 | 65.2 (11.9) |
subtype2 | 26 | 72.0 (12.0) |
subtype3 | 20 | 62.6 (11.0) |
subtype4 | 42 | 63.4 (10.4) |
subtype5 | 36 | 65.2 (12.2) |
P value = 0.378 (Chi-square test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 60 | 70 |
subtype1 | 4 | 2 |
subtype2 | 15 | 11 |
subtype3 | 8 | 12 |
subtype4 | 20 | 22 |
subtype5 | 13 | 23 |
P value = 0.157 (Chi-square test), Q value = 1
nPatients | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 117 | 10 |
subtype1 | 5 | 1 |
subtype2 | 23 | 1 |
subtype3 | 17 | 3 |
subtype4 | 36 | 5 |
subtype5 | 36 | 0 |
P value = 0.402 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 5 | 23 | 91 | 10 |
subtype1 | 1 | 0 | 5 | 0 |
subtype2 | 1 | 3 | 20 | 2 |
subtype3 | 0 | 3 | 13 | 3 |
subtype4 | 2 | 8 | 27 | 5 |
subtype5 | 1 | 9 | 26 | 0 |
P value = 0.0918 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 64 | 37 | 26 |
subtype1 | 2 | 1 | 3 |
subtype2 | 10 | 8 | 8 |
subtype3 | 6 | 8 | 5 |
subtype4 | 22 | 13 | 6 |
subtype5 | 24 | 7 | 4 |
P value = 0.0124 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1A | MX |
---|---|---|---|---|
ALL | 98 | 18 | 2 | 10 |
subtype1 | 6 | 0 | 0 | 0 |
subtype2 | 18 | 8 | 0 | 0 |
subtype3 | 15 | 1 | 2 | 1 |
subtype4 | 30 | 7 | 0 | 5 |
subtype5 | 29 | 2 | 0 | 4 |
P value = 0.218 (Chi-square test), Q value = 1
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 21 | 40 | 42 | 19 |
subtype1 | 1 | 1 | 4 | 0 |
subtype2 | 4 | 6 | 8 | 6 |
subtype3 | 2 | 3 | 10 | 3 |
subtype4 | 6 | 15 | 11 | 8 |
subtype5 | 8 | 15 | 9 | 2 |
P value = 0.785 (Chi-square test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 5 | 125 |
subtype1 | 0 | 6 |
subtype2 | 0 | 26 |
subtype3 | 1 | 19 |
subtype4 | 2 | 40 |
subtype5 | 2 | 34 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 18 | 17 | 17 | 20 |
P value = 0.66 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 43 | 4 | 0.9 - 72.1 (10.6) |
subtype1 | 11 | 1 | 1.0 - 52.0 (12.0) |
subtype2 | 9 | 1 | 1.0 - 64.0 (1.0) |
subtype3 | 11 | 2 | 0.9 - 72.1 (12.0) |
subtype4 | 12 | 0 | 0.9 - 61.9 (8.5) |
P value = 0.478 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 72 | 66.8 (10.2) |
subtype1 | 18 | 66.4 (9.5) |
subtype2 | 17 | 65.5 (10.6) |
subtype3 | 17 | 70.1 (9.2) |
subtype4 | 20 | 65.2 (11.4) |
P value = 0.586 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 33 | 39 |
subtype1 | 10 | 8 |
subtype2 | 6 | 11 |
subtype3 | 9 | 8 |
subtype4 | 8 | 12 |
P value = 0.00271 (Fisher's exact test), Q value = 0.24
nPatients | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 60 | 8 |
subtype1 | 17 | 0 |
subtype2 | 14 | 2 |
subtype3 | 17 | 0 |
subtype4 | 12 | 6 |
P value = 0.143 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 5 | 15 | 48 | 4 |
subtype1 | 2 | 3 | 12 | 1 |
subtype2 | 0 | 1 | 14 | 2 |
subtype3 | 0 | 7 | 9 | 1 |
subtype4 | 3 | 4 | 13 | 0 |
P value = 0.702 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 44 | 16 | 12 |
subtype1 | 9 | 6 | 3 |
subtype2 | 9 | 5 | 3 |
subtype3 | 12 | 2 | 3 |
subtype4 | 14 | 3 | 3 |
P value = 0.696 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 |
---|---|---|
ALL | 61 | 11 |
subtype1 | 16 | 2 |
subtype2 | 13 | 4 |
subtype3 | 14 | 3 |
subtype4 | 18 | 2 |
P value = 0.562 (Chi-square test), Q value = 1
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 18 | 25 | 18 | 10 |
subtype1 | 5 | 4 | 7 | 2 |
subtype2 | 1 | 8 | 4 | 3 |
subtype3 | 5 | 6 | 3 | 3 |
subtype4 | 7 | 7 | 4 | 2 |
P value = 0.472 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 1 | 71 |
subtype1 | 0 | 18 |
subtype2 | 1 | 16 |
subtype3 | 0 | 17 |
subtype4 | 0 | 20 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 17 | 24 | 31 |
P value = 0.382 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 43 | 4 | 0.9 - 72.1 (10.6) |
subtype1 | 11 | 1 | 1.0 - 52.0 (10.6) |
subtype2 | 13 | 0 | 0.9 - 61.9 (12.7) |
subtype3 | 19 | 3 | 0.9 - 72.1 (1.9) |
P value = 0.283 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 72 | 66.8 (10.2) |
subtype1 | 17 | 65.1 (8.0) |
subtype2 | 24 | 65.0 (12.5) |
subtype3 | 31 | 69.0 (9.3) |
P value = 0.87 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 33 | 39 |
subtype1 | 7 | 10 |
subtype2 | 12 | 12 |
subtype3 | 14 | 17 |
P value = 2.93e-05 (Fisher's exact test), Q value = 0.0026
nPatients | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 60 | 8 |
subtype1 | 16 | 0 |
subtype2 | 13 | 8 |
subtype3 | 31 | 0 |
P value = 0.709 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 5 | 15 | 48 | 4 |
subtype1 | 2 | 3 | 11 | 1 |
subtype2 | 2 | 5 | 17 | 0 |
subtype3 | 1 | 7 | 20 | 3 |
P value = 0.761 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 44 | 16 | 12 |
subtype1 | 9 | 4 | 4 |
subtype2 | 17 | 4 | 3 |
subtype3 | 18 | 8 | 5 |
P value = 0.589 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 |
---|---|---|
ALL | 61 | 11 |
subtype1 | 14 | 3 |
subtype2 | 22 | 2 |
subtype3 | 25 | 6 |
P value = 0.842 (Chi-square test), Q value = 1
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 18 | 25 | 18 | 10 |
subtype1 | 5 | 4 | 5 | 3 |
subtype2 | 7 | 10 | 5 | 2 |
subtype3 | 6 | 11 | 8 | 5 |
P value = 0.569 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 1 | 71 |
subtype1 | 0 | 17 |
subtype2 | 1 | 23 |
subtype3 | 0 | 31 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 18 | 42 | 17 | 10 | 56 |
P value = 0.314 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 106 | 10 | 0.2 - 121.1 (7.0) |
subtype1 | 16 | 3 | 0.3 - 121.1 (8.7) |
subtype2 | 38 | 5 | 0.5 - 60.0 (7.3) |
subtype3 | 15 | 0 | 0.5 - 119.5 (6.0) |
subtype4 | 10 | 0 | 0.2 - 72.1 (1.5) |
subtype5 | 27 | 2 | 0.9 - 70.0 (1.9) |
P value = 0.892 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 143 | 65.4 (11.5) |
subtype1 | 18 | 65.2 (9.4) |
subtype2 | 42 | 64.1 (12.6) |
subtype3 | 17 | 65.3 (14.5) |
subtype4 | 10 | 64.8 (7.4) |
subtype5 | 56 | 66.6 (11.1) |
P value = 0.461 (Chi-square test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 66 | 77 |
subtype1 | 8 | 10 |
subtype2 | 18 | 24 |
subtype3 | 11 | 6 |
subtype4 | 3 | 7 |
subtype5 | 26 | 30 |
P value = 0.313 (Chi-square test), Q value = 1
nPatients | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 127 | 10 |
subtype1 | 15 | 2 |
subtype2 | 40 | 1 |
subtype3 | 17 | 0 |
subtype4 | 9 | 1 |
subtype5 | 46 | 6 |
P value = 0.251 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 9 | 26 | 97 | 10 |
subtype1 | 0 | 0 | 14 | 3 |
subtype2 | 2 | 9 | 29 | 2 |
subtype3 | 3 | 3 | 9 | 2 |
subtype4 | 0 | 2 | 8 | 0 |
subtype5 | 4 | 12 | 37 | 3 |
P value = 0.0172 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 74 | 38 | 28 |
subtype1 | 5 | 4 | 7 |
subtype2 | 16 | 19 | 7 |
subtype3 | 11 | 4 | 2 |
subtype4 | 6 | 1 | 2 |
subtype5 | 36 | 10 | 10 |
P value = 0.0461 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1A | MX |
---|---|---|---|---|
ALL | 107 | 18 | 2 | 14 |
subtype1 | 11 | 2 | 1 | 3 |
subtype2 | 28 | 4 | 0 | 9 |
subtype3 | 13 | 2 | 1 | 1 |
subtype4 | 7 | 2 | 0 | 1 |
subtype5 | 48 | 8 | 0 | 0 |
P value = 0.117 (Chi-square test), Q value = 1
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 28 | 44 | 43 | 20 |
subtype1 | 0 | 5 | 6 | 3 |
subtype2 | 6 | 9 | 20 | 5 |
subtype3 | 6 | 5 | 3 | 3 |
subtype4 | 1 | 4 | 2 | 2 |
subtype5 | 15 | 21 | 12 | 7 |
P value = 0.283 (Chi-square test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 6 | 137 |
subtype1 | 2 | 16 |
subtype2 | 3 | 39 |
subtype3 | 0 | 17 |
subtype4 | 0 | 10 |
subtype5 | 1 | 55 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 20 | 64 | 59 |
P value = 0.774 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 106 | 10 | 0.2 - 121.1 (7.0) |
subtype1 | 18 | 1 | 0.2 - 64.0 (3.4) |
subtype2 | 35 | 3 | 0.9 - 72.1 (10.4) |
subtype3 | 53 | 6 | 0.2 - 121.1 (7.4) |
P value = 0.582 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 143 | 65.4 (11.5) |
subtype1 | 20 | 62.9 (13.5) |
subtype2 | 64 | 65.8 (10.4) |
subtype3 | 59 | 65.8 (12.0) |
P value = 0.973 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 66 | 77 |
subtype1 | 9 | 11 |
subtype2 | 29 | 35 |
subtype3 | 28 | 31 |
P value = 0.037 (Fisher's exact test), Q value = 1
nPatients | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 127 | 10 |
subtype1 | 19 | 1 |
subtype2 | 52 | 8 |
subtype3 | 56 | 1 |
P value = 0.726 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 9 | 26 | 97 | 10 |
subtype1 | 1 | 2 | 16 | 1 |
subtype2 | 5 | 14 | 42 | 3 |
subtype3 | 3 | 10 | 39 | 6 |
P value = 0.244 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 74 | 38 | 28 |
subtype1 | 7 | 9 | 3 |
subtype2 | 38 | 14 | 12 |
subtype3 | 29 | 15 | 13 |
P value = 0.000442 (Chi-square test), Q value = 0.039
nPatients | M0 | M1 | M1A | MX |
---|---|---|---|---|
ALL | 107 | 18 | 2 | 14 |
subtype1 | 13 | 5 | 0 | 2 |
subtype2 | 53 | 11 | 0 | 0 |
subtype3 | 41 | 2 | 2 | 12 |
P value = 0.361 (Chi-square test), Q value = 1
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 28 | 44 | 43 | 20 |
subtype1 | 2 | 5 | 7 | 5 |
subtype2 | 17 | 20 | 16 | 9 |
subtype3 | 9 | 19 | 20 | 6 |
P value = 0.298 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 6 | 137 |
subtype1 | 1 | 19 |
subtype2 | 1 | 63 |
subtype3 | 4 | 55 |
-
Cluster data file = READ-TP.mergedcluster.txt
-
Clinical data file = READ-TP.clin.merged.picked.txt
-
Number of patients = 166
-
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
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.