This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 8 different clustering approaches and 3 clinical features across 138 patients, no significant finding detected with P value < 0.05.
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4 subtypes identified in current cancer cohort by 'CN CNMF'. These subtypes do not correlate to any clinical features.
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3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes do not correlate to any clinical features.
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CNMF clustering analysis on RPPA data identified 3 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on RPPA data identified 3 subtypes that do not correlate to any clinical features.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 3 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 do not correlate to any clinical features.
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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 do not correlate to any clinical features.
Clinical Features |
Time to Death |
AGE | GENDER |
Statistical Tests | logrank test | ANOVA | Fisher's exact test |
CN CNMF | 0.349 | 0.652 | 0.279 |
METHLYATION CNMF | 0.247 | 0.291 | 0.283 |
RPPA CNMF subtypes | 0.143 | 0.365 | 0.93 |
RPPA cHierClus subtypes | 0.165 | 0.585 | 0.313 |
RNAseq CNMF subtypes | 0.322 | 0.541 | 0.701 |
RNAseq cHierClus subtypes | 0.507 | 0.316 | 0.192 |
MIRseq CNMF subtypes | 0.167 | 0.526 | 0.945 |
MIRseq cHierClus subtypes | 0.261 | 0.843 | 0.925 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 48 | 22 | 42 | 26 |
P value = 0.349 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 18 | 11 | 0.2 - 131.1 (41.8) |
subtype1 | 8 | 4 | 0.2 - 131.1 (41.8) |
subtype2 | 6 | 4 | 5.6 - 120.5 (21.2) |
subtype3 | 3 | 3 | 32.5 - 117.9 (64.4) |
subtype4 | 1 | 0 | 80.0 - 80.0 (80.0) |
P value = 0.652 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 19 | 56.8 (16.0) |
subtype1 | 8 | 61.0 (17.5) |
subtype2 | 6 | 52.7 (19.0) |
subtype3 | 3 | 53.7 (13.7) |
subtype4 | 2 | 57.0 (1.4) |
P value = 0.279 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 46 | 92 |
subtype1 | 20 | 28 |
subtype2 | 4 | 18 |
subtype3 | 13 | 29 |
subtype4 | 9 | 17 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 34 | 52 | 52 |
P value = 0.247 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 18 | 11 | 0.2 - 131.1 (41.8) |
subtype1 | 6 | 3 | 0.2 - 131.1 (52.0) |
subtype2 | 4 | 3 | 26.4 - 120.5 (90.3) |
subtype3 | 8 | 5 | 5.6 - 84.7 (29.7) |
P value = 0.291 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 19 | 56.8 (16.0) |
subtype1 | 6 | 52.3 (14.9) |
subtype2 | 4 | 68.0 (17.6) |
subtype3 | 9 | 54.8 (15.5) |
P value = 0.283 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 46 | 92 |
subtype1 | 13 | 21 |
subtype2 | 20 | 32 |
subtype3 | 13 | 39 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 40 | 34 | 25 |
P value = 0.143 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 16 | 11 | 5.6 - 131.1 (41.8) |
subtype1 | 8 | 5 | 10.1 - 131.1 (41.8) |
subtype2 | 2 | 1 | 62.8 - 80.0 (71.4) |
subtype3 | 6 | 5 | 5.6 - 84.7 (23.9) |
P value = 0.365 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 17 | 56.2 (16.9) |
subtype1 | 8 | 58.1 (17.2) |
subtype2 | 3 | 65.7 (15.0) |
subtype3 | 6 | 49.0 (16.8) |
P value = 0.93 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 35 | 64 |
subtype1 | 15 | 25 |
subtype2 | 11 | 23 |
subtype3 | 9 | 16 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 36 | 40 | 23 |
P value = 0.165 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 16 | 11 | 5.6 - 131.1 (41.8) |
subtype1 | 3 | 1 | 62.8 - 120.5 (80.0) |
subtype2 | 8 | 6 | 10.1 - 131.1 (33.3) |
subtype3 | 5 | 4 | 5.6 - 84.7 (32.5) |
P value = 0.585 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 17 | 56.2 (16.9) |
subtype1 | 3 | 62.7 (18.4) |
subtype2 | 8 | 58.0 (17.3) |
subtype3 | 6 | 50.7 (16.9) |
P value = 0.313 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 35 | 64 |
subtype1 | 14 | 22 |
subtype2 | 16 | 24 |
subtype3 | 5 | 18 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 46 | 41 | 47 |
P value = 0.322 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 16 | 10 | 0.2 - 131.1 (41.8) |
subtype1 | 7 | 5 | 0.2 - 117.9 (39.6) |
subtype2 | 4 | 3 | 12.6 - 131.1 (76.5) |
subtype3 | 5 | 2 | 10.1 - 84.7 (44.0) |
P value = 0.541 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 17 | 55.6 (16.5) |
subtype1 | 7 | 59.7 (22.1) |
subtype2 | 4 | 47.8 (11.5) |
subtype3 | 6 | 56.0 (11.5) |
P value = 0.701 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 45 | 89 |
subtype1 | 14 | 32 |
subtype2 | 16 | 25 |
subtype3 | 15 | 32 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 33 | 68 | 33 |
P value = 0.507 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 16 | 10 | 0.2 - 131.1 (41.8) |
subtype1 | 3 | 2 | 0.2 - 117.9 (62.8) |
subtype2 | 9 | 5 | 10.1 - 84.7 (39.6) |
subtype3 | 4 | 3 | 12.6 - 131.1 (76.5) |
P value = 0.316 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 17 | 55.6 (16.5) |
subtype1 | 3 | 67.3 (13.6) |
subtype2 | 10 | 55.2 (18.0) |
subtype3 | 4 | 47.8 (11.5) |
P value = 0.192 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 45 | 89 |
subtype1 | 8 | 25 |
subtype2 | 22 | 46 |
subtype3 | 15 | 18 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 57 | 45 | 31 |
P value = 0.167 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 16 | 10 | 0.2 - 131.1 (53.4) |
subtype1 | 3 | 3 | 62.8 - 117.9 (64.4) |
subtype2 | 8 | 6 | 10.1 - 131.1 (29.7) |
subtype3 | 5 | 1 | 0.2 - 120.5 (80.0) |
P value = 0.526 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 16 | 55.1 (16.6) |
subtype1 | 3 | 60.3 (22.5) |
subtype2 | 8 | 50.1 (17.1) |
subtype3 | 5 | 59.8 (13.3) |
P value = 0.945 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 44 | 89 |
subtype1 | 19 | 38 |
subtype2 | 14 | 31 |
subtype3 | 11 | 20 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 16 | 87 | 30 |
P value = 0.261 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 16 | 10 | 0.2 - 131.1 (53.4) |
subtype1 | 2 | 0 | 0.2 - 84.7 (42.5) |
subtype2 | 8 | 6 | 15.3 - 131.1 (72.4) |
subtype3 | 6 | 4 | 10.1 - 80.0 (29.7) |
P value = 0.843 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 16 | 55.1 (16.6) |
subtype1 | 2 | 56.0 (4.2) |
subtype2 | 8 | 54.1 (21.8) |
subtype3 | 6 | 56.0 (12.6) |
P value = 0.925 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 44 | 89 |
subtype1 | 6 | 10 |
subtype2 | 28 | 59 |
subtype3 | 10 | 20 |
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Cluster data file = SKCM.mergedcluster.txt
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Clinical data file = SKCM.clin.merged.picked.txt
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Number of patients = 138
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Number of clustering approaches = 8
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Number of selected clinical features = 3
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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
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.