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 57 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.
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3 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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5 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 4 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 7 subtypes that do not correlate to any clinical features.
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4 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes do not correlate to any clinical features.
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4 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes do not correlate to any clinical features.
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4 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes do not correlate to any clinical features.
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6 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 | RACE |
Statistical Tests | logrank test | Kruskal-Wallis (anova) | Fisher's exact test |
Copy Number Ratio CNMF subtypes |
0.228 (1.00) |
0.779 (1.00) |
0.733 (1.00) |
METHLYATION CNMF |
0.885 (1.00) |
0.102 (1.00) |
0.955 (1.00) |
RNAseq CNMF subtypes |
0.99 (1.00) |
0.205 (1.00) |
0.658 (1.00) |
RNAseq cHierClus subtypes |
0.0971 (1.00) |
0.234 (1.00) |
0.845 (1.00) |
MIRSEQ CNMF |
0.11 (1.00) |
0.496 (1.00) |
0.828 (1.00) |
MIRSEQ CHIERARCHICAL |
0.935 (1.00) |
0.209 (1.00) |
0.81 (1.00) |
MIRseq Mature CNMF subtypes |
0.156 (1.00) |
0.221 (1.00) |
0.266 (1.00) |
MIRseq Mature cHierClus subtypes |
0.681 (1.00) |
0.275 (1.00) |
0.634 (1.00) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 22 | 24 | 10 |
P value = 0.228 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 55 | 33 | 0.3 - 93.4 (18.1) |
subtype1 | 22 | 13 | 6.7 - 93.4 (27.0) |
subtype2 | 24 | 15 | 2.7 - 59.7 (15.3) |
subtype3 | 9 | 5 | 0.3 - 85.3 (15.8) |
P value = 0.779 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 56 | 69.8 (9.3) |
subtype1 | 22 | 69.0 (8.1) |
subtype2 | 24 | 70.8 (10.0) |
subtype3 | 10 | 69.2 (10.8) |
P value = 0.733 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 43 |
subtype1 | 1 | 5 | 15 |
subtype2 | 1 | 3 | 20 |
subtype3 | 1 | 1 | 8 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 12 | 9 | 10 | 13 | 13 |
P value = 0.885 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 56 | 34 | 0.3 - 102.4 (18.4) |
subtype1 | 12 | 8 | 0.3 - 102.4 (27.0) |
subtype2 | 9 | 6 | 4.7 - 69.6 (17.4) |
subtype3 | 10 | 7 | 5.5 - 59.4 (18.8) |
subtype4 | 12 | 6 | 2.7 - 93.4 (14.6) |
subtype5 | 13 | 7 | 3.8 - 85.3 (19.6) |
P value = 0.102 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 57 | 69.7 (9.3) |
subtype1 | 12 | 67.2 (8.0) |
subtype2 | 9 | 64.6 (6.7) |
subtype3 | 10 | 75.2 (9.2) |
subtype4 | 13 | 68.8 (9.6) |
subtype5 | 13 | 72.2 (9.8) |
P value = 0.955 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 44 |
subtype1 | 0 | 2 | 10 |
subtype2 | 0 | 1 | 8 |
subtype3 | 1 | 2 | 7 |
subtype4 | 1 | 3 | 9 |
subtype5 | 1 | 1 | 10 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 15 | 20 | 12 | 10 |
P value = 0.99 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 56 | 34 | 0.3 - 102.4 (18.4) |
subtype1 | 15 | 11 | 0.3 - 102.4 (18.8) |
subtype2 | 19 | 10 | 3.7 - 59.4 (17.8) |
subtype3 | 12 | 7 | 3.8 - 85.3 (16.5) |
subtype4 | 10 | 6 | 2.7 - 93.4 (23.9) |
P value = 0.205 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 57 | 69.7 (9.3) |
subtype1 | 15 | 69.8 (8.9) |
subtype2 | 20 | 71.9 (9.9) |
subtype3 | 12 | 70.2 (10.2) |
subtype4 | 10 | 64.7 (6.3) |
P value = 0.658 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 44 |
subtype1 | 0 | 3 | 12 |
subtype2 | 2 | 2 | 16 |
subtype3 | 1 | 1 | 9 |
subtype4 | 0 | 3 | 7 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
---|---|---|---|---|---|---|---|
Number of samples | 11 | 4 | 8 | 6 | 8 | 6 | 14 |
P value = 0.0971 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 56 | 34 | 0.3 - 102.4 (18.4) |
subtype1 | 11 | 7 | 0.3 - 102.4 (27.4) |
subtype2 | 4 | 4 | 4.7 - 22.5 (9.0) |
subtype3 | 8 | 4 | 11.9 - 59.4 (18.8) |
subtype4 | 6 | 4 | 3.8 - 85.3 (14.8) |
subtype5 | 8 | 4 | 2.7 - 69.6 (30.0) |
subtype6 | 6 | 3 | 9.8 - 55.0 (26.7) |
subtype7 | 13 | 8 | 3.7 - 93.4 (17.2) |
P value = 0.234 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 57 | 69.7 (9.3) |
subtype1 | 11 | 67.4 (8.0) |
subtype2 | 4 | 71.2 (4.3) |
subtype3 | 8 | 74.6 (8.1) |
subtype4 | 6 | 66.8 (8.4) |
subtype5 | 8 | 64.6 (6.8) |
subtype6 | 6 | 73.0 (11.9) |
subtype7 | 14 | 71.1 (11.2) |
P value = 0.845 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 44 |
subtype1 | 0 | 3 | 8 |
subtype2 | 0 | 1 | 3 |
subtype3 | 1 | 2 | 5 |
subtype4 | 0 | 0 | 5 |
subtype5 | 0 | 1 | 7 |
subtype6 | 1 | 0 | 5 |
subtype7 | 1 | 2 | 11 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 11 | 22 | 4 | 19 |
P value = 0.11 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 55 | 33 | 0.3 - 102.4 (18.1) |
subtype1 | 11 | 8 | 4.7 - 102.4 (18.1) |
subtype2 | 22 | 12 | 0.3 - 93.4 (25.0) |
subtype3 | 4 | 1 | 2.7 - 69.6 (34.9) |
subtype4 | 18 | 12 | 3.7 - 31.2 (15.5) |
P value = 0.496 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 56 | 69.8 (9.3) |
subtype1 | 11 | 69.4 (8.8) |
subtype2 | 22 | 68.5 (9.3) |
subtype3 | 4 | 67.5 (7.5) |
subtype4 | 19 | 72.0 (10.2) |
P value = 0.828 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 43 |
subtype1 | 0 | 2 | 9 |
subtype2 | 1 | 5 | 15 |
subtype3 | 0 | 0 | 4 |
subtype4 | 2 | 2 | 15 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 24 | 8 | 18 | 6 |
P value = 0.935 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 55 | 33 | 0.3 - 102.4 (18.1) |
subtype1 | 23 | 14 | 2.7 - 102.4 (17.2) |
subtype2 | 8 | 6 | 0.3 - 74.4 (27.0) |
subtype3 | 18 | 10 | 3.8 - 93.4 (23.0) |
subtype4 | 6 | 3 | 13.4 - 25.7 (16.8) |
P value = 0.209 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 56 | 69.8 (9.3) |
subtype1 | 24 | 70.9 (9.8) |
subtype2 | 8 | 67.4 (8.7) |
subtype3 | 18 | 67.7 (9.1) |
subtype4 | 6 | 74.8 (8.0) |
P value = 0.81 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 43 |
subtype1 | 1 | 3 | 20 |
subtype2 | 0 | 2 | 6 |
subtype3 | 1 | 3 | 13 |
subtype4 | 1 | 1 | 4 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 11 | 23 | 5 | 17 |
P value = 0.156 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 55 | 33 | 0.3 - 102.4 (18.1) |
subtype1 | 11 | 9 | 3.8 - 102.4 (15.5) |
subtype2 | 23 | 13 | 0.3 - 93.4 (26.6) |
subtype3 | 5 | 1 | 2.7 - 69.6 (35.8) |
subtype4 | 16 | 10 | 3.7 - 31.2 (16.5) |
P value = 0.221 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 56 | 69.8 (9.3) |
subtype1 | 11 | 68.3 (8.7) |
subtype2 | 23 | 68.4 (9.1) |
subtype3 | 5 | 68.2 (8.1) |
subtype4 | 17 | 73.2 (10.2) |
P value = 0.266 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 43 |
subtype1 | 0 | 0 | 11 |
subtype2 | 1 | 5 | 16 |
subtype3 | 0 | 2 | 3 |
subtype4 | 2 | 2 | 13 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 10 | 7 | 15 | 10 | 9 | 5 |
P value = 0.681 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 55 | 33 | 0.3 - 102.4 (18.1) |
subtype1 | 10 | 7 | 2.7 - 102.4 (8.2) |
subtype2 | 7 | 5 | 0.3 - 74.4 (27.4) |
subtype3 | 14 | 8 | 3.7 - 69.6 (19.0) |
subtype4 | 10 | 7 | 4.9 - 59.7 (25.0) |
subtype5 | 9 | 3 | 9.8 - 93.4 (17.4) |
subtype6 | 5 | 3 | 13.4 - 19.6 (15.8) |
P value = 0.275 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 56 | 69.8 (9.3) |
subtype1 | 10 | 68.1 (7.1) |
subtype2 | 7 | 67.4 (9.4) |
subtype3 | 15 | 72.2 (11.1) |
subtype4 | 10 | 68.1 (9.4) |
subtype5 | 9 | 67.7 (8.6) |
subtype6 | 5 | 76.6 (7.5) |
P value = 0.634 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 43 |
subtype1 | 0 | 2 | 8 |
subtype2 | 0 | 1 | 6 |
subtype3 | 1 | 1 | 13 |
subtype4 | 1 | 2 | 7 |
subtype5 | 0 | 3 | 5 |
subtype6 | 1 | 0 | 4 |
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Cluster data file = UCS-TP.mergedcluster.txt
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Clinical data file = UCS-TP.merged_data.txt
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Number of patients = 57
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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 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.