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 4 clinical features across 35 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.
-
2 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes do not correlate to any clinical features.
-
2 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 2 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.
-
4 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes do not correlate to any clinical features.
-
5 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes do not correlate to any clinical features.
-
7 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 |
Copy Number Ratio CNMF subtypes |
0.171 (1.00) |
0.84 (1.00) |
0.305 (1.00) |
0.48 (1.00) |
METHLYATION CNMF |
0.188 (1.00) |
0.552 (1.00) |
0.74 (1.00) |
0.124 (1.00) |
RNAseq CNMF subtypes |
0.0717 (1.00) |
0.181 (1.00) |
0.128 (1.00) |
0.169 (1.00) |
RNAseq cHierClus subtypes |
0.0591 (1.00) |
0.456 (1.00) |
0.386 (1.00) |
0.622 (1.00) |
MIRSEQ CNMF |
0.129 (1.00) |
0.79 (1.00) |
0.181 (1.00) |
0.133 (1.00) |
MIRSEQ CHIERARCHICAL |
0.34 (1.00) |
0.435 (1.00) |
0.154 (1.00) |
0.881 (1.00) |
MIRseq Mature CNMF subtypes |
0.0702 (1.00) |
0.904 (1.00) |
0.149 (1.00) |
0.151 (1.00) |
MIRseq Mature cHierClus subtypes |
0.4 (1.00) |
0.829 (1.00) |
0.211 (1.00) |
0.2 (1.00) |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 21 | 14 |
P value = 0.171 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 34 | 5 | 0.2 - 211.2 (26.0) |
subtype1 | 20 | 5 | 0.2 - 211.2 (26.0) |
subtype2 | 14 | 0 | 0.2 - 196.6 (26.0) |
P value = 0.84 (Wilcoxon-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 35 | 57.1 (11.9) |
subtype1 | 21 | 57.6 (12.1) |
subtype2 | 14 | 56.5 (12.1) |
P value = 0.305 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 18 | 17 |
subtype1 | 9 | 12 |
subtype2 | 9 | 5 |
P value = 0.48 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 18 | 1 | 16 |
subtype1 | 9 | 1 | 11 |
subtype2 | 9 | 0 | 5 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 17 | 18 |
P value = 0.188 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 34 | 5 | 0.2 - 211.2 (26.0) |
subtype1 | 16 | 1 | 0.2 - 196.6 (38.6) |
subtype2 | 18 | 4 | 0.7 - 211.2 (17.3) |
P value = 0.552 (Wilcoxon-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 35 | 57.1 (11.9) |
subtype1 | 17 | 58.8 (11.1) |
subtype2 | 18 | 55.6 (12.8) |
P value = 0.74 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 18 | 17 |
subtype1 | 8 | 9 |
subtype2 | 10 | 8 |
P value = 0.124 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 18 | 1 | 16 |
subtype1 | 6 | 1 | 10 |
subtype2 | 12 | 0 | 6 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 14 | 13 |
P value = 0.0717 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 27 | 4 | 0.2 - 211.2 (31.7) |
subtype1 | 14 | 2 | 4.3 - 211.2 (41.8) |
subtype2 | 13 | 2 | 0.2 - 98.1 (22.3) |
P value = 0.181 (Wilcoxon-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 27 | 56.3 (12.4) |
subtype1 | 14 | 59.9 (10.3) |
subtype2 | 13 | 52.4 (13.7) |
P value = 0.128 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 14 | 13 |
subtype1 | 5 | 9 |
subtype2 | 9 | 4 |
P value = 0.169 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 11 | 1 | 15 |
subtype1 | 4 | 0 | 10 |
subtype2 | 7 | 1 | 5 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 13 | 10 | 4 |
P value = 0.0591 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 27 | 4 | 0.2 - 211.2 (31.7) |
subtype1 | 13 | 2 | 4.3 - 211.2 (35.5) |
subtype2 | 10 | 2 | 0.2 - 98.1 (12.1) |
subtype3 | 4 | 0 | 15.0 - 57.2 (39.4) |
P value = 0.456 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 27 | 56.3 (12.4) |
subtype1 | 13 | 58.8 (12.7) |
subtype2 | 10 | 54.7 (13.0) |
subtype3 | 4 | 52.2 (11.6) |
P value = 0.386 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 14 | 13 |
subtype1 | 5 | 8 |
subtype2 | 6 | 4 |
subtype3 | 3 | 1 |
P value = 0.622 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 11 | 1 | 15 |
subtype1 | 5 | 0 | 8 |
subtype2 | 5 | 1 | 4 |
subtype3 | 1 | 0 | 3 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 11 | 8 | 5 | 10 |
P value = 0.129 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 33 | 5 | 0.2 - 211.2 (25.9) |
subtype1 | 11 | 1 | 0.7 - 211.2 (25.9) |
subtype2 | 7 | 1 | 0.2 - 43.9 (22.3) |
subtype3 | 5 | 1 | 9.8 - 26.0 (12.7) |
subtype4 | 10 | 2 | 4.1 - 106.1 (33.6) |
P value = 0.79 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 34 | 57.2 (12.1) |
subtype1 | 11 | 58.0 (9.9) |
subtype2 | 8 | 58.1 (10.2) |
subtype3 | 5 | 61.4 (11.9) |
subtype4 | 10 | 53.4 (16.1) |
P value = 0.181 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 17 | 17 |
subtype1 | 4 | 7 |
subtype2 | 6 | 2 |
subtype3 | 1 | 4 |
subtype4 | 6 | 4 |
P value = 0.133 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 18 | 1 | 15 |
subtype1 | 5 | 0 | 6 |
subtype2 | 4 | 1 | 3 |
subtype3 | 5 | 0 | 0 |
subtype4 | 4 | 0 | 6 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 9 | 9 | 5 | 5 | 6 |
P value = 0.34 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 33 | 5 | 0.2 - 211.2 (25.9) |
subtype1 | 9 | 1 | 4.3 - 211.2 (31.1) |
subtype2 | 8 | 2 | 0.2 - 106.1 (31.7) |
subtype3 | 5 | 0 | 0.7 - 196.6 (15.0) |
subtype4 | 5 | 1 | 9.8 - 57.2 (13.5) |
subtype5 | 6 | 1 | 4.1 - 98.1 (25.6) |
P value = 0.435 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 34 | 57.2 (12.1) |
subtype1 | 9 | 56.3 (10.4) |
subtype2 | 9 | 59.1 (10.0) |
subtype3 | 5 | 55.8 (11.3) |
subtype4 | 5 | 65.4 (8.2) |
subtype5 | 6 | 49.8 (18.3) |
P value = 0.154 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 17 | 17 |
subtype1 | 2 | 7 |
subtype2 | 6 | 3 |
subtype3 | 2 | 3 |
subtype4 | 2 | 3 |
subtype5 | 5 | 1 |
P value = 0.881 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 18 | 1 | 15 |
subtype1 | 4 | 0 | 5 |
subtype2 | 4 | 1 | 4 |
subtype3 | 3 | 0 | 2 |
subtype4 | 4 | 0 | 1 |
subtype5 | 3 | 0 | 3 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 13 | 18 |
P value = 0.0702 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 30 | 5 | 0.2 - 211.2 (26.0) |
subtype1 | 13 | 1 | 0.7 - 211.2 (24.7) |
subtype2 | 17 | 4 | 0.2 - 106.1 (35.5) |
P value = 0.904 (Wilcoxon-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 31 | 56.3 (12.2) |
subtype1 | 13 | 56.5 (11.0) |
subtype2 | 18 | 56.2 (13.3) |
P value = 0.149 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 15 | 16 |
subtype1 | 4 | 9 |
subtype2 | 11 | 7 |
P value = 0.151 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 16 | 1 | 14 |
subtype1 | 9 | 0 | 4 |
subtype2 | 7 | 1 | 10 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 |
---|---|---|---|---|---|---|---|---|
Number of samples | 3 | 4 | 3 | 4 | 8 | 3 | 4 | 2 |
P value = 0.4 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 28 | 4 | 0.2 - 211.2 (25.3) |
subtype1 | 3 | 0 | 0.8 - 22.3 (4.3) |
subtype2 | 3 | 0 | 0.2 - 42.7 (4.3) |
subtype3 | 3 | 0 | 15.0 - 196.6 (25.9) |
subtype4 | 4 | 1 | 10.3 - 26.0 (13.1) |
subtype5 | 8 | 1 | 0.7 - 211.2 (29.2) |
subtype6 | 3 | 1 | 35.5 - 106.1 (52.0) |
subtype7 | 4 | 1 | 4.6 - 43.9 (27.8) |
P value = 0.829 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 29 | 56.9 (12.3) |
subtype1 | 3 | 61.0 (13.5) |
subtype2 | 4 | 62.5 (11.6) |
subtype3 | 3 | 56.7 (14.6) |
subtype4 | 4 | 58.2 (11.0) |
subtype5 | 8 | 51.6 (12.1) |
subtype6 | 3 | 54.7 (23.1) |
subtype7 | 4 | 59.5 (7.1) |
P value = 0.211 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 14 | 15 |
subtype1 | 2 | 1 |
subtype2 | 2 | 2 |
subtype3 | 0 | 3 |
subtype4 | 1 | 3 |
subtype5 | 4 | 4 |
subtype6 | 1 | 2 |
subtype7 | 4 | 0 |
P value = 0.2 (Fisher's exact test), Q value = 1
nPatients | ASIAN | WHITE |
---|---|---|
ALL | 16 | 13 |
subtype1 | 2 | 1 |
subtype2 | 1 | 3 |
subtype3 | 1 | 2 |
subtype4 | 4 | 0 |
subtype5 | 6 | 2 |
subtype6 | 1 | 2 |
subtype7 | 1 | 3 |
-
Cluster data file = DLBC-TP.mergedcluster.txt
-
Clinical data file = DLBC-TP.merged_data.txt
-
Number of patients = 35
-
Number of clustering approaches = 8
-
Number of selected clinical features = 4
-
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.