This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 6 different clustering approaches and 9 clinical features across 162 patients, 6 significant findings detected with P value < 0.05.
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3 subtypes identified in current cancer cohort by 'CN CNMF'. These subtypes correlate to 'GENDER' and 'PATHOLOGY.T'.
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3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'PATHOLOGY.T'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 2 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'PATHOLOGY.N' and 'TUMOR.STAGE'.
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CNMF clustering analysis on sequencing-based miR expression data identified 3 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 'HISTOLOGICAL.TYPE'.
Clinical Features |
Statistical Tests |
CN CNMF |
METHLYATION CNMF |
RNAseq CNMF subtypes |
RNAseq cHierClus subtypes |
MIRseq CNMF subtypes |
MIRseq cHierClus subtypes |
Time to Death | logrank test | 0.142 | 0.694 | 0.667 | 0.8 | 0.223 | 0.895 |
AGE | ANOVA | 0.129 | 0.141 | 0.143 | 0.447 | 0.119 | 0.599 |
GENDER | Fisher's exact test | 0.0167 | 0.927 | 0.547 | 0.917 | 0.693 | 0.62 |
HISTOLOGICAL TYPE | Chi-square test | 0.319 | 0.142 | 0.0766 | 0.407 | 0.109 | 0.0114 |
PATHOLOGY T | Chi-square test | 0.00471 | 0.02 | 0.242 | 0.425 | 0.181 | 0.265 |
PATHOLOGY N | Chi-square test | 0.765 | 0.658 | 0.174 | 0.0334 | 0.755 | 0.112 |
PATHOLOGICSPREAD(M) | Chi-square test | 0.186 | 0.361 | 0.327 | 0.474 | 0.48 | 0.691 |
TUMOR STAGE | Chi-square test | 0.527 | 0.176 | 0.0535 | 0.00304 | 0.246 | 0.295 |
RADIATIONS RADIATION REGIMENINDICATION | Fisher's exact test | 1 | 0.521 | 0.0701 | 0.213 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 21 | 73 | 67 |
P value = 0.142 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 124 | 16 | 0.1 - 72.2 (1.5) |
subtype1 | 10 | 3 | 0.9 - 29.0 (8.8) |
subtype2 | 57 | 7 | 0.1 - 72.2 (4.3) |
subtype3 | 57 | 6 | 0.1 - 70.1 (1.0) |
P value = 0.129 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 154 | 67.7 (10.6) |
subtype1 | 20 | 71.5 (9.1) |
subtype2 | 69 | 68.2 (9.9) |
subtype3 | 65 | 66.1 (11.5) |
P value = 0.0167 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 65 | 96 |
subtype1 | 12 | 9 |
subtype2 | 21 | 52 |
subtype3 | 32 | 35 |
P value = 0.319 (Chi-square test)
nPatients | STOMACH ADENOCARCINOMA - DIFFUSE TYPE | STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS) | STOMACH ADENOCARCINOMA - SIGNET RING TYPE | STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE | STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS) |
---|---|---|---|---|---|---|---|
ALL | 19 | 79 | 1 | 9 | 3 | 10 | 35 |
subtype1 | 1 | 14 | 0 | 1 | 0 | 0 | 5 |
subtype2 | 9 | 30 | 0 | 4 | 2 | 9 | 16 |
subtype3 | 9 | 35 | 1 | 4 | 1 | 1 | 14 |
P value = 0.00471 (Chi-square test)
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 6 | 53 | 59 | 33 |
subtype1 | 3 | 8 | 5 | 2 |
subtype2 | 1 | 29 | 29 | 10 |
subtype3 | 2 | 16 | 25 | 21 |
P value = 0.765 (Chi-square test)
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 50 | 57 | 24 | 19 |
subtype1 | 7 | 6 | 3 | 0 |
subtype2 | 22 | 25 | 12 | 10 |
subtype3 | 21 | 26 | 9 | 9 |
P value = 0.186 (Chi-square test)
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 132 | 18 | 11 |
subtype1 | 21 | 0 | 0 |
subtype2 | 60 | 8 | 5 |
subtype3 | 51 | 10 | 6 |
P value = 0.527 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 25 | 43 | 48 | 29 |
subtype1 | 3 | 5 | 7 | 0 |
subtype2 | 12 | 21 | 19 | 15 |
subtype3 | 10 | 17 | 22 | 14 |
P value = 1 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 5 | 156 |
subtype1 | 0 | 21 |
subtype2 | 3 | 70 |
subtype3 | 2 | 65 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 29 | 35 | 33 |
P value = 0.694 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 88 | 11 | 0.1 - 72.2 (1.6) |
subtype1 | 27 | 4 | 0.1 - 65.1 (1.7) |
subtype2 | 31 | 3 | 0.1 - 70.1 (1.2) |
subtype3 | 30 | 4 | 0.2 - 72.2 (3.3) |
P value = 0.141 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 90 | 67.3 (10.9) |
subtype1 | 27 | 70.0 (10.9) |
subtype2 | 34 | 64.5 (11.6) |
subtype3 | 29 | 68.0 (9.5) |
P value = 0.927 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 32 | 65 |
subtype1 | 10 | 19 |
subtype2 | 12 | 23 |
subtype3 | 10 | 23 |
P value = 0.142 (Chi-square test)
nPatients | STOMACH ADENOCARCINOMA - DIFFUSE TYPE | STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS) | STOMACH ADENOCARCINOMA - SIGNET RING TYPE | STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE | STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS) |
---|---|---|---|---|---|---|---|
ALL | 15 | 44 | 1 | 6 | 3 | 9 | 19 |
subtype1 | 5 | 10 | 0 | 2 | 1 | 3 | 8 |
subtype2 | 8 | 20 | 1 | 2 | 0 | 0 | 4 |
subtype3 | 2 | 14 | 0 | 2 | 2 | 6 | 7 |
P value = 0.02 (Chi-square test)
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 4 | 38 | 45 | 10 |
subtype1 | 4 | 11 | 10 | 4 |
subtype2 | 0 | 10 | 21 | 4 |
subtype3 | 0 | 17 | 14 | 2 |
P value = 0.658 (Chi-square test)
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 38 | 31 | 17 | 11 |
subtype1 | 15 | 8 | 3 | 3 |
subtype2 | 10 | 13 | 8 | 4 |
subtype3 | 13 | 10 | 6 | 4 |
P value = 0.361 (Chi-square test)
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 81 | 9 | 7 |
subtype1 | 26 | 1 | 2 |
subtype2 | 27 | 6 | 2 |
subtype3 | 28 | 2 | 3 |
P value = 0.176 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 18 | 33 | 31 | 15 |
subtype1 | 10 | 9 | 7 | 3 |
subtype2 | 3 | 12 | 12 | 8 |
subtype3 | 5 | 12 | 12 | 4 |
P value = 0.521 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 5 | 92 |
subtype1 | 1 | 28 |
subtype2 | 1 | 34 |
subtype3 | 3 | 30 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 22 | 21 |
P value = 0.667 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 18 | 5 | 1.0 - 54.0 (14.0) |
subtype1 | 7 | 2 | 1.0 - 22.0 (12.0) |
subtype2 | 11 | 3 | 1.0 - 54.0 (18.9) |
P value = 0.143 (t-test)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 43 | 70.4 (10.5) |
subtype1 | 22 | 68.1 (11.6) |
subtype2 | 21 | 72.8 (8.8) |
P value = 0.547 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 20 | 23 |
subtype1 | 9 | 13 |
subtype2 | 11 | 10 |
P value = 0.0766 (Chi-square test)
nPatients | STOMACH ADENOCARCINOMA - DIFFUSE TYPE | STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS) | STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS) |
---|---|---|---|---|---|
ALL | 2 | 25 | 1 | 1 | 9 |
subtype1 | 1 | 15 | 1 | 1 | 1 |
subtype2 | 1 | 10 | 0 | 0 | 8 |
P value = 0.242 (Chi-square test)
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 2 | 14 | 9 | 9 |
subtype1 | 0 | 6 | 6 | 6 |
subtype2 | 2 | 8 | 3 | 3 |
P value = 0.174 (Chi-square test)
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 8 | 14 | 5 | 5 |
subtype1 | 2 | 10 | 2 | 2 |
subtype2 | 6 | 4 | 3 | 3 |
P value = 0.327 (Chi-square test)
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 34 | 7 | 2 |
subtype1 | 16 | 4 | 2 |
subtype2 | 18 | 3 | 0 |
P value = 0.0535 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 7 | 4 | 6 | 11 |
subtype1 | 1 | 4 | 3 | 6 |
subtype2 | 6 | 0 | 3 | 5 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 15 | 7 | 21 |
P value = 0.8 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 18 | 5 | 1.0 - 54.0 (14.0) |
subtype1 | 9 | 3 | 1.0 - 54.0 (18.9) |
subtype2 | 2 | 0 | 1.0 - 30.0 (15.5) |
subtype3 | 7 | 2 | 1.0 - 22.0 (12.0) |
P value = 0.447 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 43 | 70.4 (10.5) |
subtype1 | 15 | 72.8 (8.9) |
subtype2 | 7 | 66.9 (11.4) |
subtype3 | 21 | 69.8 (11.2) |
P value = 0.917 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 20 | 23 |
subtype1 | 8 | 7 |
subtype2 | 3 | 4 |
subtype3 | 9 | 12 |
P value = 0.407 (Chi-square test)
nPatients | STOMACH ADENOCARCINOMA - DIFFUSE TYPE | STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS) | STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS) |
---|---|---|---|---|---|
ALL | 2 | 25 | 1 | 1 | 9 |
subtype1 | 1 | 7 | 0 | 0 | 5 |
subtype2 | 0 | 4 | 0 | 0 | 3 |
subtype3 | 1 | 14 | 1 | 1 | 1 |
P value = 0.425 (Chi-square test)
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 2 | 14 | 9 | 9 |
subtype1 | 1 | 6 | 3 | 3 |
subtype2 | 1 | 3 | 1 | 0 |
subtype3 | 0 | 5 | 5 | 6 |
P value = 0.0334 (Chi-square test)
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 8 | 14 | 5 | 5 |
subtype1 | 3 | 2 | 3 | 3 |
subtype2 | 4 | 2 | 0 | 0 |
subtype3 | 1 | 10 | 2 | 2 |
P value = 0.474 (Chi-square test)
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 34 | 7 | 2 |
subtype1 | 12 | 3 | 0 |
subtype2 | 6 | 0 | 1 |
subtype3 | 16 | 4 | 1 |
P value = 0.00304 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 7 | 4 | 6 | 11 |
subtype1 | 3 | 0 | 3 | 5 |
subtype2 | 4 | 0 | 0 | 0 |
subtype3 | 0 | 4 | 3 | 6 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 51 | 34 | 49 |
P value = 0.223 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 97 | 15 | 0.1 - 72.2 (3.0) |
subtype1 | 44 | 10 | 0.1 - 54.0 (4.0) |
subtype2 | 24 | 1 | 0.1 - 70.1 (1.2) |
subtype3 | 29 | 4 | 0.1 - 72.2 (4.1) |
P value = 0.119 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 127 | 68.0 (10.9) |
subtype1 | 49 | 66.8 (10.7) |
subtype2 | 34 | 66.3 (12.9) |
subtype3 | 44 | 70.8 (9.1) |
P value = 0.693 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 52 | 82 |
subtype1 | 22 | 29 |
subtype2 | 13 | 21 |
subtype3 | 17 | 32 |
P value = 0.109 (Chi-square test)
nPatients | STOMACH ADENOCARCINOMA - DIFFUSE TYPE | STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS) | STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE | STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS) |
---|---|---|---|---|---|---|
ALL | 14 | 69 | 7 | 3 | 10 | 26 |
subtype1 | 6 | 20 | 2 | 1 | 6 | 16 |
subtype2 | 5 | 22 | 2 | 0 | 0 | 4 |
subtype3 | 3 | 27 | 3 | 2 | 4 | 6 |
P value = 0.181 (Chi-square test)
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 6 | 51 | 50 | 17 |
subtype1 | 2 | 20 | 23 | 6 |
subtype2 | 0 | 11 | 16 | 3 |
subtype3 | 4 | 20 | 11 | 8 |
P value = 0.755 (Chi-square test)
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 43 | 46 | 21 | 13 |
subtype1 | 19 | 16 | 9 | 4 |
subtype2 | 11 | 13 | 6 | 2 |
subtype3 | 13 | 17 | 6 | 7 |
P value = 0.48 (Chi-square test)
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 114 | 14 | 6 |
subtype1 | 43 | 6 | 2 |
subtype2 | 30 | 4 | 0 |
subtype3 | 41 | 4 | 4 |
P value = 0.246 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 24 | 35 | 34 | 25 |
subtype1 | 8 | 17 | 14 | 9 |
subtype2 | 4 | 12 | 8 | 6 |
subtype3 | 12 | 6 | 12 | 10 |
P value = 0.0701 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 5 | 129 |
subtype1 | 0 | 51 |
subtype2 | 1 | 33 |
subtype3 | 4 | 45 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 43 | 34 | 57 |
P value = 0.895 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 97 | 15 | 0.1 - 72.2 (3.0) |
subtype1 | 32 | 4 | 0.1 - 70.1 (1.2) |
subtype2 | 26 | 4 | 0.3 - 55.0 (4.1) |
subtype3 | 39 | 7 | 0.1 - 72.2 (4.0) |
P value = 0.599 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 127 | 68.0 (10.9) |
subtype1 | 42 | 66.7 (12.9) |
subtype2 | 31 | 68.3 (9.4) |
subtype3 | 54 | 68.9 (10.2) |
P value = 0.62 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 52 | 82 |
subtype1 | 15 | 28 |
subtype2 | 12 | 22 |
subtype3 | 25 | 32 |
P value = 0.0114 (Chi-square test)
nPatients | STOMACH ADENOCARCINOMA - DIFFUSE TYPE | STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS) | STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE | STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS) |
---|---|---|---|---|---|---|
ALL | 14 | 69 | 7 | 3 | 10 | 26 |
subtype1 | 6 | 26 | 3 | 0 | 0 | 6 |
subtype2 | 2 | 14 | 1 | 2 | 8 | 7 |
subtype3 | 6 | 29 | 3 | 1 | 2 | 13 |
P value = 0.265 (Chi-square test)
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 6 | 51 | 50 | 17 |
subtype1 | 1 | 13 | 17 | 8 |
subtype2 | 0 | 14 | 14 | 4 |
subtype3 | 5 | 24 | 19 | 5 |
P value = 0.112 (Chi-square test)
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 43 | 46 | 21 | 13 |
subtype1 | 13 | 19 | 7 | 2 |
subtype2 | 8 | 8 | 9 | 5 |
subtype3 | 22 | 19 | 5 | 6 |
P value = 0.691 (Chi-square test)
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 114 | 14 | 6 |
subtype1 | 36 | 6 | 1 |
subtype2 | 30 | 3 | 1 |
subtype3 | 48 | 5 | 4 |
P value = 0.295 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 24 | 35 | 34 | 25 |
subtype1 | 6 | 13 | 10 | 10 |
subtype2 | 4 | 11 | 7 | 8 |
subtype3 | 14 | 11 | 17 | 7 |
P value = 0.213 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 5 | 129 |
subtype1 | 1 | 42 |
subtype2 | 3 | 31 |
subtype3 | 1 | 56 |
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Cluster data file = STAD-TP.mergedcluster.txt
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Clinical data file = STAD-TP.clin.merged.picked.txt
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Number of patients = 162
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Number of clustering approaches = 6
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Number of selected clinical features = 9
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Exclude small clusters that include fewer than K patients, K = 3
consensus non-negative matrix factorization clustering approach (Brunet et al. 2004)
Resampling-based clustering method (Monti et al. 2003)
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For continuous numerical clinical features, one-way analysis of variance (Howell 2002) was applied to compare the clinical values between tumor subtypes using 'anova' function in R
For 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 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
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.