This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 7 different clustering approaches and 4 clinical features across 33 patients, no 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 '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 do not correlate to any clinical features.
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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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5 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes do not correlate to any clinical features.
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3 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes do not correlate to any clinical features.
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5 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 | GENDER | RACE |
Statistical Tests | logrank test | Kruskal-Wallis (anova) | Fisher's exact test | Fisher's exact test |
METHLYATION CNMF |
0.205 (1.00) |
0.428 (1.00) |
0.732 (1.00) |
0.0525 (1.00) |
RNAseq CNMF subtypes |
0.0302 (0.845) |
0.288 (1.00) |
0.111 (1.00) |
0.308 (1.00) |
RNAseq cHierClus subtypes |
0.0302 (0.845) |
0.559 (1.00) |
0.482 (1.00) |
0.776 (1.00) |
MIRSEQ CNMF |
0.0458 (1.00) |
0.954 (1.00) |
0.682 (1.00) |
0.825 (1.00) |
MIRSEQ CHIERARCHICAL |
0.443 (1.00) |
0.939 (1.00) |
0.623 (1.00) |
0.146 (1.00) |
MIRseq Mature CNMF subtypes |
0.434 (1.00) |
0.892 (1.00) |
0.512 (1.00) |
0.907 (1.00) |
MIRseq Mature cHierClus subtypes |
0.428 (1.00) |
0.861 (1.00) |
0.769 (1.00) |
0.939 (1.00) |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 16 | 17 |
P value = 0.205 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 32 | 5 | 0.2 - 211.2 (25.4) |
subtype1 | 15 | 1 | 0.2 - 196.6 (26.7) |
subtype2 | 17 | 4 | 0.4 - 211.2 (15.0) |
P value = 0.428 (Wilcoxon-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 33 | 57.2 (12.2) |
subtype1 | 16 | 59.3 (11.3) |
subtype2 | 17 | 55.1 (13.0) |
P value = 0.732 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 18 | 15 |
subtype1 | 8 | 8 |
subtype2 | 10 | 7 |
P value = 0.0525 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 17 | 1 | 15 |
subtype1 | 5 | 1 | 10 |
subtype2 | 12 | 0 | 5 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 13 | 12 |
P value = 0.0302 (logrank test), Q value = 0.84
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 25 | 4 | 0.2 - 211.2 (29.9) |
subtype1 | 13 | 2 | 4.3 - 211.2 (46.3) |
subtype2 | 12 | 2 | 0.2 - 74.1 (20.9) |
P value = 0.288 (Wilcoxon-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 25 | 56.2 (12.8) |
subtype1 | 13 | 59.7 (10.7) |
subtype2 | 12 | 52.5 (14.3) |
P value = 0.111 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 14 | 11 |
subtype1 | 5 | 8 |
subtype2 | 9 | 3 |
P value = 0.308 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 10 | 1 | 14 |
subtype1 | 4 | 0 | 9 |
subtype2 | 6 | 1 | 5 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 12 | 9 | 4 |
P value = 0.0302 (logrank test), Q value = 0.84
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 25 | 4 | 0.2 - 211.2 (29.9) |
subtype1 | 12 | 2 | 4.3 - 211.2 (41.5) |
subtype2 | 9 | 2 | 0.2 - 74.1 (4.6) |
subtype3 | 4 | 0 | 15.0 - 46.3 (25.7) |
P value = 0.559 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 25 | 56.2 (12.8) |
subtype1 | 12 | 58.4 (13.2) |
subtype2 | 9 | 55.1 (13.7) |
subtype3 | 4 | 52.2 (11.6) |
P value = 0.482 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 14 | 11 |
subtype1 | 5 | 7 |
subtype2 | 6 | 3 |
subtype3 | 3 | 1 |
P value = 0.776 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 10 | 1 | 14 |
subtype1 | 5 | 0 | 7 |
subtype2 | 4 | 1 | 4 |
subtype3 | 1 | 0 | 3 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 11 | 13 |
P value = 0.0458 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 24 | 4 | 0.2 - 211.2 (28.6) |
subtype1 | 11 | 1 | 4.3 - 211.2 (31.1) |
subtype2 | 13 | 3 | 0.2 - 106.1 (22.3) |
P value = 0.954 (Wilcoxon-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 24 | 56.2 (13.1) |
subtype1 | 11 | 57.3 (11.6) |
subtype2 | 13 | 55.4 (14.7) |
P value = 0.682 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 13 | 11 |
subtype1 | 5 | 6 |
subtype2 | 8 | 5 |
P value = 0.825 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 10 | 1 | 13 |
subtype1 | 4 | 0 | 7 |
subtype2 | 6 | 1 | 6 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 |
---|---|---|---|---|---|---|---|---|
Number of samples | 2 | 2 | 3 | 4 | 5 | 2 | 3 | 3 |
P value = 0.443 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 18 | 4 | 0.2 - 211.2 (33.6) |
subtype3 | 3 | 0 | 15.0 - 196.6 (46.3) |
subtype4 | 4 | 0 | 0.2 - 29.9 (11.3) |
subtype5 | 5 | 1 | 4.6 - 74.1 (31.7) |
subtype7 | 3 | 1 | 4.1 - 211.2 (52.0) |
subtype8 | 3 | 2 | 41.2 - 106.1 (47.4) |
P value = 0.939 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 18 | 55.9 (13.7) |
subtype3 | 3 | 57.7 (15.3) |
subtype4 | 4 | 61.2 (8.2) |
subtype5 | 5 | 52.2 (19.4) |
subtype7 | 3 | 55.0 (15.7) |
subtype8 | 3 | 54.0 (12.1) |
P value = 0.623 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 10 | 8 |
subtype3 | 1 | 2 |
subtype4 | 3 | 1 |
subtype5 | 4 | 1 |
subtype7 | 1 | 2 |
subtype8 | 1 | 2 |
P value = 0.146 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 8 | 1 | 9 |
subtype3 | 1 | 0 | 2 |
subtype4 | 4 | 0 | 0 |
subtype5 | 2 | 0 | 3 |
subtype7 | 1 | 0 | 2 |
subtype8 | 0 | 1 | 2 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 6 | 9 | 9 |
P value = 0.434 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 24 | 4 | 0.2 - 211.2 (28.6) |
subtype1 | 6 | 0 | 4.3 - 196.6 (27.0) |
subtype2 | 9 | 2 | 0.2 - 106.1 (24.7) |
subtype3 | 9 | 2 | 4.1 - 211.2 (31.7) |
P value = 0.892 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 24 | 56.2 (13.1) |
subtype1 | 6 | 57.8 (14.2) |
subtype2 | 9 | 57.8 (10.1) |
subtype3 | 9 | 53.7 (15.9) |
P value = 0.512 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 13 | 11 |
subtype1 | 2 | 4 |
subtype2 | 5 | 4 |
subtype3 | 6 | 3 |
P value = 0.907 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 10 | 1 | 13 |
subtype1 | 2 | 0 | 4 |
subtype2 | 4 | 1 | 4 |
subtype3 | 4 | 0 | 5 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |
---|---|---|---|---|---|---|---|---|---|
Number of samples | 2 | 3 | 3 | 2 | 3 | 2 | 4 | 3 | 2 |
P value = 0.428 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 16 | 3 | 0.2 - 211.2 (28.2) |
subtype2 | 3 | 0 | 0.2 - 24.7 (4.3) |
subtype3 | 3 | 0 | 15.0 - 196.6 (46.3) |
subtype5 | 3 | 1 | 22.3 - 106.1 (35.5) |
subtype7 | 4 | 1 | 4.6 - 74.1 (25.6) |
subtype8 | 3 | 1 | 4.1 - 211.2 (52.0) |
P value = 0.861 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 16 | 57.0 (14.6) |
subtype2 | 3 | 62.0 (14.2) |
subtype3 | 3 | 57.7 (15.3) |
subtype5 | 3 | 51.7 (20.8) |
subtype7 | 4 | 58.2 (16.0) |
subtype8 | 3 | 55.0 (15.7) |
P value = 0.769 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 8 | 8 |
subtype2 | 1 | 2 |
subtype3 | 1 | 2 |
subtype5 | 2 | 1 |
subtype7 | 3 | 1 |
subtype8 | 1 | 2 |
P value = 0.939 (Fisher's exact test), Q value = 1
nPatients | ASIAN | WHITE |
---|---|---|
ALL | 6 | 10 |
subtype2 | 1 | 2 |
subtype3 | 1 | 2 |
subtype5 | 2 | 1 |
subtype7 | 1 | 3 |
subtype8 | 1 | 2 |
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Cluster data file = DLBC-TP.mergedcluster.txt
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Clinical data file = DLBC-TP.merged_data.txt
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Number of patients = 33
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Number of clustering approaches = 7
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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 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.