This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 7 different clustering approaches and 7 clinical features across 143 patients, 13 significant findings detected with P value < 0.05.
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CNMF clustering analysis on array-based mRNA expression data identified 3 subtypes that correlate to 'HISTOLOGICAL.TYPE'.
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Consensus hierarchical clustering analysis on array-based mRNA expression data identified 3 subtypes that correlate to 'HISTOLOGICAL.TYPE'.
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4 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'Time to Death', 'AGE', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'Time to Death' and 'HISTOLOGICAL.TYPE'.
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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 do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on sequencing-based miR expression data identified 4 subtypes that correlate to 'AGE', 'GENDER', and 'HISTOLOGICAL.TYPE'.
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
NEOADJUVANT THERAPY |
Statistical Tests | logrank test | ANOVA | Fisher's exact test | ANOVA | Chi-square test | Fisher's exact test | Fisher's exact test |
mRNA CNMF subtypes | 0.0944 | 0.326 | 0.101 | 0.441 | 0.0226 | 0.384 | 0.883 |
mRNA cHierClus subtypes | 0.126 | 0.467 | 0.172 | 0.441 | 0.0136 | 0.757 | 0.685 |
METHLYATION CNMF | 1.73e-06 | 1.38e-05 | 0.0696 | 0.845 | 3.33e-10 | 6.96e-05 | 0.459 |
RNAseq CNMF subtypes | 0.0355 | 0.0914 | 0.306 | 0.826 | 0.000403 | 0.201 | 0.661 |
RNAseq cHierClus subtypes | 0.0635 | 0.0294 | 0.214 | 0.842 | 0.000268 | 0.366 | 0.281 |
MIRseq CNMF subtypes | 0.195 | 0.285 | 0.172 | 0.719 | 0.469 | 0.79 | 0.102 |
MIRseq cHierClus subtypes | 0.112 | 0.0293 | 0.0238 | 0.729 | 0.00256 | 0.339 | 0.0789 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 9 | 10 | 8 |
P value = 0.0944 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 27 | 9 | 0.1 - 134.3 (46.6) |
subtype1 | 9 | 4 | 10.6 - 130.8 (43.9) |
subtype2 | 10 | 3 | 0.1 - 78.2 (36.5) |
subtype3 | 8 | 2 | 14.4 - 134.3 (51.3) |
P value = 0.326 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 27 | 39.3 (9.1) |
subtype1 | 9 | 39.2 (6.2) |
subtype2 | 10 | 42.3 (7.6) |
subtype3 | 8 | 35.8 (12.6) |
P value = 0.101 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 9 | 18 |
subtype1 | 2 | 7 |
subtype2 | 6 | 4 |
subtype3 | 1 | 7 |
P value = 0.441 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 17 | 88.8 (12.2) |
subtype1 | 7 | 84.3 (16.2) |
subtype2 | 7 | 92.9 (7.6) |
subtype3 | 3 | 90.0 (10.0) |
P value = 0.0226 (Chi-square test)
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 10 | 9 | 8 |
subtype1 | 7 | 2 | 0 |
subtype2 | 2 | 3 | 5 |
subtype3 | 1 | 4 | 3 |
P value = 0.384 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 19 | 8 |
subtype1 | 7 | 2 |
subtype2 | 8 | 2 |
subtype3 | 4 | 4 |
P value = 0.883 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 17 | 10 |
subtype1 | 5 | 4 |
subtype2 | 7 | 3 |
subtype3 | 5 | 3 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 9 | 7 | 11 |
P value = 0.126 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 27 | 9 | 0.1 - 134.3 (46.6) |
subtype1 | 9 | 4 | 10.6 - 130.8 (43.9) |
subtype2 | 7 | 2 | 14.4 - 134.3 (52.4) |
subtype3 | 11 | 3 | 0.1 - 78.2 (41.1) |
P value = 0.467 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 27 | 39.3 (9.1) |
subtype1 | 9 | 39.2 (6.2) |
subtype2 | 7 | 36.0 (13.6) |
subtype3 | 11 | 41.5 (7.6) |
P value = 0.172 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 9 | 18 |
subtype1 | 2 | 7 |
subtype2 | 1 | 6 |
subtype3 | 6 | 5 |
P value = 0.441 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 17 | 88.8 (12.2) |
subtype1 | 7 | 84.3 (16.2) |
subtype2 | 3 | 90.0 (10.0) |
subtype3 | 7 | 92.9 (7.6) |
P value = 0.0136 (Chi-square test)
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 10 | 9 | 8 |
subtype1 | 7 | 2 | 0 |
subtype2 | 0 | 4 | 3 |
subtype3 | 3 | 3 | 5 |
P value = 0.757 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 19 | 8 |
subtype1 | 7 | 2 |
subtype2 | 4 | 3 |
subtype3 | 8 | 3 |
P value = 0.685 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 17 | 10 |
subtype1 | 5 | 4 |
subtype2 | 4 | 3 |
subtype3 | 8 | 3 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 63 | 23 | 16 | 38 |
P value = 1.73e-06 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 140 | 44 | 0.0 - 211.2 (17.8) |
subtype1 | 63 | 19 | 0.0 - 156.2 (23.3) |
subtype2 | 23 | 15 | 0.9 - 211.2 (11.5) |
subtype3 | 16 | 2 | 0.1 - 97.9 (14.3) |
subtype4 | 38 | 8 | 0.1 - 182.3 (26.1) |
P value = 1.38e-05 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 140 | 42.6 (13.0) |
subtype1 | 63 | 38.8 (11.4) |
subtype2 | 23 | 51.7 (13.7) |
subtype3 | 16 | 36.2 (13.0) |
subtype4 | 38 | 46.0 (11.2) |
P value = 0.0696 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 62 | 78 |
subtype1 | 22 | 41 |
subtype2 | 15 | 8 |
subtype3 | 6 | 10 |
subtype4 | 19 | 19 |
P value = 0.845 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 76 | 89.2 (10.3) |
subtype1 | 38 | 90.0 (10.1) |
subtype2 | 14 | 87.9 (5.8) |
subtype3 | 6 | 86.7 (10.3) |
subtype4 | 18 | 89.4 (13.5) |
P value = 3.33e-10 (Chi-square test)
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 49 | 34 | 56 |
subtype1 | 27 | 21 | 14 |
subtype2 | 14 | 6 | 3 |
subtype3 | 6 | 5 | 5 |
subtype4 | 2 | 2 | 34 |
P value = 6.96e-05 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 83 | 57 |
subtype1 | 48 | 15 |
subtype2 | 16 | 7 |
subtype3 | 5 | 11 |
subtype4 | 14 | 24 |
P value = 0.459 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 70 | 70 |
subtype1 | 32 | 31 |
subtype2 | 12 | 11 |
subtype3 | 5 | 11 |
subtype4 | 21 | 17 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 13 | 17 | 17 |
P value = 0.0355 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 47 | 24 | 1.2 - 211.2 (31.8) |
subtype1 | 13 | 9 | 6.7 - 211.2 (16.8) |
subtype2 | 17 | 8 | 6.8 - 94.5 (43.9) |
subtype3 | 17 | 7 | 1.2 - 182.3 (47.9) |
P value = 0.0914 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 47 | 44.0 (12.3) |
subtype1 | 13 | 46.4 (14.6) |
subtype2 | 17 | 38.8 (7.4) |
subtype3 | 17 | 47.3 (13.2) |
P value = 0.306 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 25 | 22 |
subtype1 | 9 | 4 |
subtype2 | 7 | 10 |
subtype3 | 9 | 8 |
P value = 0.826 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 27 | 89.6 (10.9) |
subtype1 | 9 | 90.0 (5.0) |
subtype2 | 10 | 88.0 (14.8) |
subtype3 | 8 | 91.2 (11.3) |
P value = 0.000403 (Chi-square test)
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 15 | 14 | 18 |
subtype1 | 8 | 4 | 1 |
subtype2 | 7 | 6 | 4 |
subtype3 | 0 | 4 | 13 |
P value = 0.201 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 33 | 14 |
subtype1 | 10 | 3 |
subtype2 | 14 | 3 |
subtype3 | 9 | 8 |
P value = 0.661 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 26 | 21 |
subtype1 | 7 | 6 |
subtype2 | 8 | 9 |
subtype3 | 11 | 6 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 12 | 16 | 19 |
P value = 0.0635 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 47 | 24 | 1.2 - 211.2 (31.8) |
subtype1 | 12 | 8 | 6.7 - 211.2 (15.1) |
subtype2 | 16 | 6 | 1.2 - 182.3 (43.1) |
subtype3 | 19 | 10 | 6.8 - 114.0 (47.9) |
P value = 0.0294 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 47 | 44.0 (12.3) |
subtype1 | 12 | 46.8 (15.2) |
subtype2 | 16 | 48.6 (12.3) |
subtype3 | 19 | 38.4 (7.8) |
P value = 0.214 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 25 | 22 |
subtype1 | 9 | 3 |
subtype2 | 8 | 8 |
subtype3 | 8 | 11 |
P value = 0.842 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 27 | 89.6 (10.9) |
subtype1 | 8 | 90.0 (5.3) |
subtype2 | 7 | 91.4 (12.1) |
subtype3 | 12 | 88.3 (13.4) |
P value = 0.000268 (Chi-square test)
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 15 | 14 | 18 |
subtype1 | 7 | 4 | 1 |
subtype2 | 0 | 3 | 13 |
subtype3 | 8 | 7 | 4 |
P value = 0.366 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 33 | 14 |
subtype1 | 9 | 3 |
subtype2 | 9 | 7 |
subtype3 | 15 | 4 |
P value = 0.281 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 26 | 21 |
subtype1 | 7 | 5 |
subtype2 | 11 | 5 |
subtype3 | 8 | 11 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 22 | 25 | 20 |
P value = 0.195 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 67 | 27 | 0.1 - 211.2 (23.8) |
subtype1 | 22 | 12 | 4.7 - 182.3 (19.4) |
subtype2 | 25 | 9 | 0.1 - 134.3 (46.6) |
subtype3 | 20 | 6 | 1.2 - 211.2 (16.3) |
P value = 0.285 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 67 | 43.1 (12.1) |
subtype1 | 22 | 42.7 (11.2) |
subtype2 | 25 | 40.8 (9.6) |
subtype3 | 20 | 46.5 (15.2) |
P value = 0.172 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 33 | 34 |
subtype1 | 14 | 8 |
subtype2 | 9 | 16 |
subtype3 | 10 | 10 |
P value = 0.719 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 41 | 89.8 (9.6) |
subtype1 | 13 | 89.2 (7.6) |
subtype2 | 16 | 88.8 (12.6) |
subtype3 | 12 | 91.7 (7.2) |
P value = 0.469 (Chi-square test)
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 24 | 20 | 23 |
subtype1 | 8 | 7 | 7 |
subtype2 | 10 | 9 | 6 |
subtype3 | 6 | 4 | 10 |
P value = 0.79 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 48 | 19 |
subtype1 | 17 | 5 |
subtype2 | 17 | 8 |
subtype3 | 14 | 6 |
P value = 0.102 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 39 | 28 |
subtype1 | 9 | 13 |
subtype2 | 18 | 7 |
subtype3 | 12 | 8 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 25 | 15 | 13 | 14 |
P value = 0.112 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 67 | 27 | 0.1 - 211.2 (23.8) |
subtype1 | 25 | 9 | 0.1 - 134.3 (46.6) |
subtype2 | 15 | 8 | 6.4 - 211.2 (13.4) |
subtype3 | 13 | 6 | 4.7 - 114.0 (18.9) |
subtype4 | 14 | 4 | 1.2 - 182.3 (24.1) |
P value = 0.0293 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 67 | 43.1 (12.1) |
subtype1 | 25 | 40.1 (9.1) |
subtype2 | 15 | 47.8 (12.4) |
subtype3 | 13 | 38.0 (9.3) |
subtype4 | 14 | 48.3 (15.6) |
P value = 0.0238 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 33 | 34 |
subtype1 | 8 | 17 |
subtype2 | 11 | 4 |
subtype3 | 9 | 4 |
subtype4 | 5 | 9 |
P value = 0.729 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 41 | 89.8 (9.6) |
subtype1 | 16 | 88.8 (12.6) |
subtype2 | 12 | 88.3 (5.8) |
subtype3 | 8 | 92.5 (4.6) |
subtype4 | 5 | 92.0 (13.0) |
P value = 0.00256 (Chi-square test)
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 24 | 20 | 23 |
subtype1 | 11 | 9 | 5 |
subtype2 | 9 | 4 | 2 |
subtype3 | 4 | 4 | 5 |
subtype4 | 0 | 3 | 11 |
P value = 0.339 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 48 | 19 |
subtype1 | 17 | 8 |
subtype2 | 13 | 2 |
subtype3 | 10 | 3 |
subtype4 | 8 | 6 |
P value = 0.0789 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 39 | 28 |
subtype1 | 19 | 6 |
subtype2 | 9 | 6 |
subtype3 | 5 | 8 |
subtype4 | 6 | 8 |
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Cluster data file = LGG.mergedcluster.txt
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Clinical data file = LGG.clin.merged.picked.txt
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Number of patients = 143
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Number of clustering approaches = 7
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Number of selected clinical features = 7
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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
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.