This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 5 different clustering approaches and 6 clinical features across 177 patients, 13 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 mRNA expression data identified 4 subtypes that correlate to 'AGE' and 'HISTOLOGICAL.TYPE'.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'AGE', 'GENDER', 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' 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', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
Clinical Features |
Statistical Tests |
METHLYATION CNMF |
RNAseq CNMF subtypes |
RNAseq cHierClus subtypes |
MIRseq CNMF subtypes |
MIRseq cHierClus subtypes |
Time to Death | logrank test | 0.0253 | 0.157 | 0.157 | 0.0455 | 0.0455 |
AGE | ANOVA | 0.00306 | 0.0347 | 0.00234 | 0.444 | 0.47 |
GENDER | Fisher's exact test | 0.938 | 0.133 | 0.000857 | 0.356 | 0.444 |
HISTOLOGICAL TYPE | Chi-square test | 6.57e-11 | 1.53e-08 | 1.54e-10 | 1.05e-14 | 4.66e-13 |
RADIATIONS RADIATION REGIMENINDICATION | Fisher's exact test | 0.102 | 0.0801 | 0.215 | 0.124 | 0.00996 |
NEOADJUVANT THERAPY | Fisher's exact test | 1 | 1 | 0.586 | 0.513 | 0.389 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 43 | 23 | 91 |
P value = 0.0253 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 157 | 1 | 0.1 - 66.1 (9.0) |
subtype1 | 43 | 1 | 0.2 - 65.9 (7.7) |
subtype2 | 23 | 0 | 0.1 - 66.1 (6.8) |
subtype3 | 91 | 0 | 0.2 - 66.1 (10.4) |
P value = 0.00306 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 157 | 46.7 (15.9) |
subtype1 | 43 | 53.5 (16.8) |
subtype2 | 23 | 42.0 (14.1) |
subtype3 | 91 | 44.7 (15.0) |
P value = 0.938 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 113 | 44 |
subtype1 | 30 | 13 |
subtype2 | 17 | 6 |
subtype3 | 66 | 25 |
P value = 6.57e-11 (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 | 4 | 91 | 43 | 19 |
subtype1 | 4 | 9 | 28 | 2 |
subtype2 | 0 | 15 | 5 | 3 |
subtype3 | 0 | 67 | 10 | 14 |
P value = 0.102 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 14 | 143 |
subtype1 | 1 | 42 |
subtype2 | 1 | 22 |
subtype3 | 12 | 79 |
P value = 1 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 3 | 154 |
subtype1 | 1 | 42 |
subtype2 | 0 | 23 |
subtype3 | 2 | 89 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 34 | 27 | 42 | 13 |
P value = 0.157 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 116 | 1 | 0.1 - 65.9 (8.9) |
subtype1 | 34 | 1 | 0.3 - 65.9 (7.4) |
subtype2 | 27 | 0 | 0.5 - 65.7 (9.6) |
subtype3 | 42 | 0 | 1.0 - 65.9 (10.2) |
subtype4 | 13 | 0 | 0.1 - 65.9 (9.2) |
P value = 0.0347 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 116 | 47.7 (16.3) |
subtype1 | 34 | 54.2 (17.3) |
subtype2 | 27 | 42.9 (13.5) |
subtype3 | 42 | 46.6 (16.2) |
subtype4 | 13 | 44.4 (15.4) |
P value = 0.133 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 81 | 35 |
subtype1 | 23 | 11 |
subtype2 | 23 | 4 |
subtype3 | 25 | 17 |
subtype4 | 10 | 3 |
P value = 1.53e-08 (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 | 3 | 65 | 32 | 16 |
subtype1 | 3 | 7 | 23 | 1 |
subtype2 | 0 | 21 | 4 | 2 |
subtype3 | 0 | 29 | 3 | 10 |
subtype4 | 0 | 8 | 2 | 3 |
P value = 0.0801 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 11 | 105 |
subtype1 | 1 | 33 |
subtype2 | 1 | 26 |
subtype3 | 8 | 34 |
subtype4 | 1 | 12 |
P value = 1 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 3 | 113 |
subtype1 | 1 | 33 |
subtype2 | 1 | 26 |
subtype3 | 1 | 41 |
subtype4 | 0 | 13 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 31 | 64 | 21 |
P value = 0.157 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 116 | 1 | 0.1 - 65.9 (8.9) |
subtype1 | 31 | 1 | 0.3 - 65.9 (7.6) |
subtype2 | 64 | 0 | 0.1 - 65.9 (9.4) |
subtype3 | 21 | 0 | 0.5 - 65.7 (9.0) |
P value = 0.00234 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 116 | 47.7 (16.3) |
subtype1 | 31 | 56.1 (16.2) |
subtype2 | 64 | 45.3 (15.7) |
subtype3 | 21 | 42.5 (14.3) |
P value = 0.000857 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 81 | 35 |
subtype1 | 20 | 11 |
subtype2 | 40 | 24 |
subtype3 | 21 | 0 |
P value = 1.54e-10 (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 | 3 | 65 | 32 | 16 |
subtype1 | 3 | 5 | 22 | 1 |
subtype2 | 0 | 45 | 5 | 14 |
subtype3 | 0 | 15 | 5 | 1 |
P value = 0.215 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 11 | 105 |
subtype1 | 1 | 30 |
subtype2 | 9 | 55 |
subtype3 | 1 | 20 |
P value = 0.586 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 3 | 113 |
subtype1 | 1 | 30 |
subtype2 | 1 | 63 |
subtype3 | 1 | 20 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 47 | 56 | 47 |
P value = 0.0455 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 150 | 1 | 0.1 - 66.1 (8.1) |
subtype1 | 47 | 1 | 0.3 - 65.9 (7.2) |
subtype2 | 56 | 0 | 0.2 - 66.1 (11.1) |
subtype3 | 47 | 0 | 0.1 - 66.1 (8.0) |
P value = 0.444 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 150 | 46.6 (15.7) |
subtype1 | 47 | 48.8 (17.1) |
subtype2 | 56 | 44.8 (15.2) |
subtype3 | 47 | 46.6 (14.9) |
P value = 0.356 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 108 | 42 |
subtype1 | 31 | 16 |
subtype2 | 44 | 12 |
subtype3 | 33 | 14 |
P value = 1.05e-14 (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 | 78 | 50 | 16 |
subtype1 | 5 | 5 | 36 | 1 |
subtype2 | 0 | 42 | 9 | 5 |
subtype3 | 1 | 31 | 5 | 10 |
P value = 0.124 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 14 | 136 |
subtype1 | 2 | 45 |
subtype2 | 9 | 47 |
subtype3 | 3 | 44 |
P value = 0.513 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 3 | 147 |
subtype1 | 2 | 45 |
subtype2 | 1 | 55 |
subtype3 | 0 | 47 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 43 | 55 | 52 |
P value = 0.0455 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 150 | 1 | 0.1 - 66.1 (8.1) |
subtype1 | 43 | 1 | 0.3 - 65.9 (7.1) |
subtype2 | 55 | 0 | 0.1 - 66.1 (9.2) |
subtype3 | 52 | 0 | 0.2 - 66.1 (9.4) |
P value = 0.47 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 150 | 46.6 (15.7) |
subtype1 | 43 | 49.0 (16.6) |
subtype2 | 55 | 46.1 (15.2) |
subtype3 | 52 | 45.1 (15.5) |
P value = 0.444 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 108 | 42 |
subtype1 | 29 | 14 |
subtype2 | 43 | 12 |
subtype3 | 36 | 16 |
P value = 4.66e-13 (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 | 78 | 50 | 16 |
subtype1 | 5 | 5 | 32 | 1 |
subtype2 | 0 | 34 | 9 | 12 |
subtype3 | 1 | 39 | 9 | 3 |
P value = 0.00996 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 14 | 136 |
subtype1 | 1 | 42 |
subtype2 | 3 | 52 |
subtype3 | 10 | 42 |
P value = 0.389 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 3 | 147 |
subtype1 | 1 | 42 |
subtype2 | 0 | 55 |
subtype3 | 2 | 50 |
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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 = 177
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Number of clustering approaches = 5
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Number of selected clinical features = 6
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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.