This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 3 different clustering approaches and 4 clinical features across 137 patients, 8 significant findings detected with P value < 0.05.
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3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'Time to Death', 'AGE', and 'HISTOLOGICAL.TYPE'.
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CNMF clustering analysis on sequencing-based miR expression data identified 3 subtypes that correlate to 'Time to Death', 'AGE', and 'HISTOLOGICAL.TYPE'.
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Consensus hierarchical clustering analysis on sequencing-based miR expression data identified 3 subtypes that correlate to 'Time to Death' and 'HISTOLOGICAL.TYPE'.
Clinical Features |
Statistical Tests |
METHLYATION CNMF |
MIRseq CNMF subtypes |
MIRseq cHierClus subtypes |
Time to Death | logrank test | 0.0279 | 0.019 | 0.00563 |
AGE | ANOVA | 0.000287 | 0.0441 | 0.162 |
GENDER | Fisher's exact test | 0.862 | 0.405 | 0.699 |
HISTOLOGICAL TYPE | Chi-square test | 9.59e-09 | 1.65e-07 | 7.31e-07 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 39 | 20 | 78 |
P value = 0.0279 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 137 | 1 | 0.1 - 66.1 (9.0) |
subtype1 | 39 | 1 | 0.2 - 65.9 (7.6) |
subtype2 | 20 | 0 | 0.1 - 66.1 (6.4) |
subtype3 | 78 | 0 | 0.2 - 66.1 (12.3) |
P value = 0.000287 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 137 | 45.4 (16.3) |
subtype1 | 39 | 53.7 (17.6) |
subtype2 | 20 | 38.1 (13.0) |
subtype3 | 78 | 43.2 (15.0) |
P value = 0.862 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 38 | 99 |
subtype1 | 12 | 27 |
subtype2 | 5 | 15 |
subtype3 | 21 | 57 |
P value = 9.59e-09 (Chi-square test)
nPatients | OTHER | THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL | THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) | THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) |
---|---|---|---|---|
ALL | 7 | 76 | 39 | 15 |
subtype1 | 4 | 7 | 26 | 2 |
subtype2 | 1 | 14 | 4 | 1 |
subtype3 | 2 | 55 | 9 | 12 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 32 | 46 | 31 |
P value = 0.019 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 109 | 1 | 0.1 - 66.1 (8.1) |
subtype1 | 32 | 1 | 0.3 - 47.4 (7.8) |
subtype2 | 46 | 0 | 0.2 - 66.1 (19.2) |
subtype3 | 31 | 0 | 0.1 - 65.9 (6.8) |
P value = 0.0441 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 109 | 45.6 (16.1) |
subtype1 | 32 | 51.2 (18.4) |
subtype2 | 46 | 41.9 (13.8) |
subtype3 | 31 | 45.2 (15.8) |
P value = 0.405 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 33 | 76 |
subtype1 | 12 | 20 |
subtype2 | 11 | 35 |
subtype3 | 10 | 21 |
P value = 1.65e-07 (Chi-square test)
nPatients | OTHER | THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL | THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) | THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) |
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ALL | 6 | 57 | 34 | 12 |
subtype1 | 3 | 4 | 23 | 2 |
subtype2 | 2 | 32 | 8 | 4 |
subtype3 | 1 | 21 | 3 | 6 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 29 | 37 | 43 |
P value = 0.00563 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 109 | 1 | 0.1 - 66.1 (8.1) |
subtype1 | 29 | 1 | 0.3 - 46.7 (7.7) |
subtype2 | 37 | 0 | 0.2 - 66.1 (8.2) |
subtype3 | 43 | 0 | 0.1 - 66.0 (12.3) |
P value = 0.162 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 109 | 45.6 (16.1) |
subtype1 | 29 | 50.5 (18.4) |
subtype2 | 37 | 43.8 (14.2) |
subtype3 | 43 | 43.8 (15.8) |
P value = 0.699 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 33 | 76 |
subtype1 | 10 | 19 |
subtype2 | 12 | 25 |
subtype3 | 11 | 32 |
P value = 7.31e-07 (Chi-square test)
nPatients | OTHER | THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL | THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) | THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) |
---|---|---|---|---|
ALL | 6 | 57 | 34 | 12 |
subtype1 | 3 | 4 | 21 | 1 |
subtype2 | 1 | 26 | 7 | 3 |
subtype3 | 2 | 27 | 6 | 8 |
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Cluster data file = THCA.mergedcluster.txt
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Clinical data file = THCA.clin.merged.picked.txt
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Number of patients = 137
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Number of clustering approaches = 3
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Number of selected clinical features = 4
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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.