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 7 clinical features across 21 patients, one significant finding detected with P value < 0.05 and Q value < 0.25.
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2 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes do not correlate to any clinical features.
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2 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 sequencing-based mRNA expression data identified 2 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 correlate to 'Time to Death'.
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2 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes do not correlate to any clinical features.
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3 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes do not correlate to any clinical features.
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
Statistical Tests | logrank test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test |
Copy Number Ratio CNMF subtypes |
0.142 (1.00) |
0.165 (1.00) |
0.938 (1.00) |
0.0318 (1.00) |
1 (1.00) |
0.44 (1.00) |
1 (1.00) |
METHLYATION CNMF |
0.419 (1.00) |
0.672 (1.00) |
0.0701 (1.00) |
0.387 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
RNAseq CNMF subtypes |
0.109 (1.00) |
0.274 (1.00) |
0.0305 (1.00) |
0.0805 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
RNAseq cHierClus subtypes |
0.00209 (0.117) |
0.125 (1.00) |
0.71 (1.00) |
0.352 (1.00) |
0.0746 (1.00) |
1 (1.00) |
0.67 (1.00) |
MIRSEQ CNMF |
0.332 (1.00) |
0.0711 (1.00) |
0.286 (1.00) |
0.315 (1.00) |
0.58 (1.00) |
0.759 (1.00) |
0.308 (1.00) |
MIRSEQ CHIERARCHICAL |
0.312 (1.00) |
0.585 (1.00) |
0.785 (1.00) |
0.743 (1.00) |
0.678 (1.00) |
1 (1.00) |
0.134 (1.00) |
MIRseq Mature CNMF subtypes |
0.48 (1.00) |
0.247 (1.00) |
1 (1.00) |
0.619 (1.00) |
0.282 (1.00) |
0.57 (1.00) |
0.282 (1.00) |
MIRseq Mature cHierClus subtypes |
0.73 (1.00) |
0.881 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.107 (1.00) |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 9 | 12 |
P value = 0.142 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 21 | 16 | 0.2 - 91.7 (17.3) |
subtype1 | 9 | 7 | 1.9 - 23.9 (17.3) |
subtype2 | 12 | 9 | 0.2 - 91.7 (20.0) |
P value = 0.165 (Wilcoxon-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 21 | 63.6 (7.5) |
subtype1 | 9 | 60.9 (5.5) |
subtype2 | 12 | 65.7 (8.3) |
P value = 0.938 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|---|
ALL | 1 | 1 | 6 | 11 | 2 |
subtype1 | 0 | 0 | 2 | 6 | 1 |
subtype2 | 1 | 1 | 4 | 5 | 1 |
P value = 0.0318 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 13 | 8 |
subtype1 | 3 | 6 |
subtype2 | 10 | 2 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 14 | 6 |
subtype1 | 6 | 3 |
subtype2 | 8 | 3 |
P value = 0.44 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 15 | 1 | 5 |
subtype1 | 8 | 0 | 1 |
subtype2 | 7 | 1 | 4 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 6 | 15 |
subtype1 | 3 | 6 |
subtype2 | 3 | 9 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 11 | 10 |
P value = 0.419 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 21 | 16 | 0.2 - 91.7 (17.3) |
subtype1 | 11 | 8 | 8.0 - 91.7 (17.9) |
subtype2 | 10 | 8 | 0.2 - 80.8 (9.5) |
P value = 0.672 (Wilcoxon-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 21 | 63.6 (7.5) |
subtype1 | 11 | 62.8 (7.7) |
subtype2 | 10 | 64.5 (7.5) |
P value = 0.0701 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|---|
ALL | 1 | 1 | 6 | 11 | 2 |
subtype1 | 0 | 0 | 5 | 4 | 2 |
subtype2 | 1 | 1 | 1 | 7 | 0 |
P value = 0.387 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 13 | 8 |
subtype1 | 8 | 3 |
subtype2 | 5 | 5 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 14 | 6 |
subtype1 | 8 | 3 |
subtype2 | 6 | 3 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 15 | 1 | 5 |
subtype1 | 7 | 1 | 3 |
subtype2 | 8 | 0 | 2 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 6 | 15 |
subtype1 | 3 | 8 |
subtype2 | 3 | 7 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 11 | 10 |
P value = 0.109 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 21 | 16 | 0.2 - 91.7 (17.3) |
subtype1 | 11 | 8 | 8.0 - 91.7 (18.8) |
subtype2 | 10 | 8 | 0.2 - 51.8 (9.5) |
P value = 0.274 (Wilcoxon-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 21 | 63.6 (7.5) |
subtype1 | 11 | 61.7 (7.9) |
subtype2 | 10 | 65.7 (6.8) |
P value = 0.0305 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|---|
ALL | 1 | 1 | 6 | 11 | 2 |
subtype1 | 1 | 0 | 5 | 3 | 2 |
subtype2 | 0 | 1 | 1 | 8 | 0 |
P value = 0.0805 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 13 | 8 |
subtype1 | 9 | 2 |
subtype2 | 4 | 6 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 14 | 6 |
subtype1 | 8 | 3 |
subtype2 | 6 | 3 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 15 | 1 | 5 |
subtype1 | 7 | 1 | 3 |
subtype2 | 8 | 0 | 2 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 6 | 15 |
subtype1 | 3 | 8 |
subtype2 | 3 | 7 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 11 | 4 | 6 |
P value = 0.00209 (logrank test), Q value = 0.12
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 21 | 16 | 0.2 - 91.7 (17.3) |
subtype1 | 11 | 8 | 1.9 - 91.7 (17.9) |
subtype2 | 4 | 3 | 18.8 - 51.8 (23.6) |
subtype3 | 6 | 5 | 0.2 - 17.3 (6.6) |
P value = 0.125 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 21 | 63.6 (7.5) |
subtype1 | 11 | 62.8 (7.9) |
subtype2 | 4 | 58.5 (5.8) |
subtype3 | 6 | 68.5 (5.4) |
P value = 0.71 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|---|
ALL | 1 | 1 | 6 | 11 | 2 |
subtype1 | 1 | 0 | 4 | 4 | 2 |
subtype2 | 0 | 0 | 1 | 3 | 0 |
subtype3 | 0 | 1 | 1 | 4 | 0 |
P value = 0.352 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 13 | 8 |
subtype1 | 8 | 3 |
subtype2 | 3 | 1 |
subtype3 | 2 | 4 |
P value = 0.0746 (Fisher's exact test), Q value = 1
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 14 | 6 |
subtype1 | 8 | 3 |
subtype2 | 1 | 3 |
subtype3 | 5 | 0 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 15 | 1 | 5 |
subtype1 | 7 | 1 | 3 |
subtype2 | 3 | 0 | 1 |
subtype3 | 5 | 0 | 1 |
P value = 0.67 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 6 | 15 |
subtype1 | 3 | 8 |
subtype2 | 2 | 2 |
subtype3 | 1 | 5 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 9 | 7 |
P value = 0.332 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 16 | 12 | 0.2 - 51.8 (14.3) |
subtype1 | 9 | 7 | 1.9 - 51.8 (17.9) |
subtype2 | 7 | 5 | 0.2 - 23.9 (12.2) |
P value = 0.0711 (Wilcoxon-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 16 | 63.8 (6.9) |
subtype1 | 9 | 61.2 (8.2) |
subtype2 | 7 | 67.1 (2.4) |
P value = 0.286 (Fisher's exact test), Q value = 1
nPatients | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 1 | 3 | 10 | 2 |
subtype1 | 0 | 3 | 5 | 1 |
subtype2 | 1 | 0 | 5 | 1 |
P value = 0.315 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 8 | 8 |
subtype1 | 6 | 3 |
subtype2 | 2 | 5 |
P value = 0.58 (Fisher's exact test), Q value = 1
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 10 | 5 |
subtype1 | 5 | 4 |
subtype2 | 5 | 1 |
P value = 0.759 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 12 | 1 | 3 |
subtype1 | 7 | 0 | 2 |
subtype2 | 5 | 1 | 1 |
P value = 0.308 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 5 | 11 |
subtype1 | 4 | 5 |
subtype2 | 1 | 6 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
---|---|---|---|---|---|---|---|
Number of samples | 3 | 3 | 4 | 2 | 2 | 1 | 1 |
P value = 0.312 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 10 | 7 | 0.2 - 31.2 (11.6) |
subtype1 | 3 | 2 | 13.6 - 31.2 (17.9) |
subtype2 | 3 | 2 | 1.9 - 12.2 (10.9) |
subtype3 | 4 | 3 | 0.2 - 23.9 (4.4) |
P value = 0.585 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 10 | 65.3 (7.0) |
subtype1 | 3 | 61.3 (7.1) |
subtype2 | 3 | 67.3 (11.0) |
subtype3 | 4 | 66.8 (3.3) |
P value = 0.785 (Fisher's exact test), Q value = 1
nPatients | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 1 | 2 | 6 | 1 |
subtype1 | 0 | 1 | 1 | 1 |
subtype2 | 0 | 1 | 2 | 0 |
subtype3 | 1 | 0 | 3 | 0 |
P value = 0.743 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 4 | 6 |
subtype1 | 2 | 1 |
subtype2 | 1 | 2 |
subtype3 | 1 | 3 |
P value = 0.678 (Fisher's exact test), Q value = 1
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 6 | 3 |
subtype1 | 1 | 2 |
subtype2 | 3 | 0 |
subtype3 | 2 | 1 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 8 | 2 |
subtype1 | 2 | 1 |
subtype2 | 3 | 0 |
subtype3 | 3 | 1 |
P value = 0.134 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2 | 8 |
subtype1 | 0 | 3 |
subtype2 | 2 | 1 |
subtype3 | 0 | 4 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 8 | 8 |
P value = 0.48 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 16 | 12 | 0.2 - 51.8 (14.3) |
subtype1 | 8 | 7 | 1.9 - 51.8 (18.4) |
subtype2 | 8 | 5 | 0.2 - 23.9 (12.9) |
P value = 0.247 (Wilcoxon-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 16 | 63.8 (6.9) |
subtype1 | 8 | 62.0 (8.3) |
subtype2 | 8 | 65.6 (4.8) |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 1 | 3 | 10 | 2 |
subtype1 | 0 | 2 | 5 | 1 |
subtype2 | 1 | 1 | 5 | 1 |
P value = 0.619 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 8 | 8 |
subtype1 | 5 | 3 |
subtype2 | 3 | 5 |
P value = 0.282 (Fisher's exact test), Q value = 1
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 10 | 5 |
subtype1 | 4 | 4 |
subtype2 | 6 | 1 |
P value = 0.57 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 12 | 1 | 3 |
subtype1 | 7 | 0 | 1 |
subtype2 | 5 | 1 | 2 |
P value = 0.282 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 5 | 11 |
subtype1 | 4 | 4 |
subtype2 | 1 | 7 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 2 | 3 | 5 | 2 | 2 | 2 |
P value = 0.73 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 8 | 6 | 0.2 - 23.9 (8.1) |
subtype2 | 3 | 2 | 1.9 - 12.2 (10.9) |
subtype3 | 5 | 4 | 0.2 - 23.9 (5.2) |
P value = 0.881 (Wilcoxon-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 8 | 67.1 (6.3) |
subtype2 | 3 | 67.3 (11.0) |
subtype3 | 5 | 67.0 (2.9) |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 1 | 1 | 5 | 1 |
subtype2 | 0 | 1 | 2 | 0 |
subtype3 | 1 | 0 | 3 | 1 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 3 | 5 |
subtype2 | 1 | 2 |
subtype3 | 2 | 3 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 6 | 1 |
subtype2 | 3 | 0 |
subtype3 | 3 | 1 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 6 | 1 | 1 |
subtype2 | 3 | 0 | 0 |
subtype3 | 3 | 1 | 1 |
P value = 0.107 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2 | 6 |
subtype2 | 2 | 1 |
subtype3 | 0 | 5 |
-
Cluster data file = MESO-TP.mergedcluster.txt
-
Clinical data file = MESO-TP.merged_data.txt
-
Number of patients = 21
-
Number of clustering approaches = 8
-
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 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 multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.