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 3 clinical features across 137 patients, no significant finding detected with P value < 0.05.
-
4 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes do not correlate to any clinical features.
-
CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that do not correlate to any clinical features.
-
Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that do not correlate to any clinical features.
-
CNMF clustering analysis on sequencing-based miR expression data identified 3 subtypes that do not correlate to any clinical features.
-
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 |
METHLYATION CNMF | 0.413 | 0.313 | 0.0695 |
RNAseq CNMF subtypes | 0.14 | 0.786 | 0.374 |
RNAseq cHierClus subtypes | 0.644 | 0.189 | 0.762 |
MIRseq CNMF subtypes | 0.167 | 0.526 | 0.917 |
MIRseq cHierClus subtypes | 0.261 | 0.843 | 0.923 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 15 | 37 | 46 | 38 |
P value = 0.413 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 17 | 11 | 5.6 - 131.1 (44.0) |
subtype1 | 4 | 3 | 12.6 - 131.1 (52.0) |
subtype2 | 3 | 2 | 62.8 - 117.9 (80.3) |
subtype3 | 7 | 4 | 5.6 - 84.7 (27.0) |
subtype4 | 3 | 2 | 26.4 - 120.5 (32.5) |
P value = 0.313 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 18 | 56.7 (16.5) |
subtype1 | 4 | 47.8 (16.8) |
subtype2 | 3 | 69.0 (12.3) |
subtype3 | 8 | 53.8 (16.2) |
subtype4 | 3 | 64.0 (17.5) |
P value = 0.0695 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 45 | 91 |
subtype1 | 3 | 12 |
subtype2 | 15 | 22 |
subtype3 | 10 | 36 |
subtype4 | 17 | 21 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 43 | 40 | 42 |
P value = 0.14 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 15 | 10 | 10.1 - 131.1 (44.0) |
subtype1 | 5 | 5 | 15.3 - 117.9 (62.8) |
subtype2 | 6 | 4 | 10.1 - 131.1 (36.0) |
subtype3 | 4 | 1 | 27.0 - 84.7 (62.0) |
P value = 0.786 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 16 | 55.4 (17.0) |
subtype1 | 5 | 57.4 (26.3) |
subtype2 | 6 | 51.3 (13.5) |
subtype3 | 5 | 58.2 (11.3) |
P value = 0.374 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 43 | 82 |
subtype1 | 12 | 31 |
subtype2 | 17 | 23 |
subtype3 | 14 | 28 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 57 | 31 | 37 |
P value = 0.644 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 15 | 10 | 10.1 - 131.1 (44.0) |
subtype1 | 6 | 3 | 15.3 - 84.7 (54.2) |
subtype2 | 3 | 2 | 39.6 - 117.9 (62.8) |
subtype3 | 6 | 5 | 10.1 - 131.1 (29.7) |
P value = 0.189 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 16 | 55.4 (17.0) |
subtype1 | 7 | 51.1 (18.0) |
subtype2 | 3 | 71.7 (11.5) |
subtype3 | 6 | 52.2 (15.1) |
P value = 0.762 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 43 | 82 |
subtype1 | 21 | 36 |
subtype2 | 9 | 22 |
subtype3 | 13 | 24 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 56 | 46 | 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 = 0.917 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 44 | 89 |
subtype1 | 19 | 37 |
subtype2 | 14 | 32 |
subtype3 | 11 | 20 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 16 | 29 | 88 |
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 | 6 | 4 | 10.1 - 80.0 (29.7) |
subtype3 | 8 | 6 | 15.3 - 131.1 (72.4) |
P value = 0.843 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 16 | 55.1 (16.6) |
subtype1 | 2 | 56.0 (4.2) |
subtype2 | 6 | 56.0 (12.6) |
subtype3 | 8 | 54.1 (21.8) |
P value = 0.923 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 44 | 89 |
subtype1 | 6 | 10 |
subtype2 | 9 | 20 |
subtype3 | 29 | 59 |
-
Cluster data file = SKCM.mergedcluster.txt
-
Clinical data file = SKCM.clin.merged.picked.txt
-
Number of patients = 137
-
Number of clustering approaches = 5
-
Number of selected clinical features = 3
-
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.