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 8 clinical features across 48 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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3 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 3 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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4 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes do not correlate to any clinical features.
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2 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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3 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 |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
NUMBER OF LYMPH NODES |
TUMOR STAGECODE |
Statistical Tests | logrank test | ANOVA | Fisher's exact test | ANOVA | Fisher's exact test | Fisher's exact test | ANOVA | ANOVA |
Copy Number Ratio CNMF subtypes |
0.251 (1.00) |
0.687 (1.00) |
0.301 (1.00) |
0.641 (1.00) |
0.324 (1.00) |
0.583 (1.00) |
0.202 (1.00) |
|
METHLYATION CNMF |
0.482 (1.00) |
0.979 (1.00) |
0.59 (1.00) |
0.402 (1.00) |
0.315 (1.00) |
0.316 (1.00) |
0.264 (1.00) |
|
RNAseq CNMF subtypes |
0.977 (1.00) |
0.589 (1.00) |
0.424 (1.00) |
0.412 (1.00) |
0.0517 (1.00) |
0.9 (1.00) |
0.18 (1.00) |
|
RNAseq cHierClus subtypes |
0.577 (1.00) |
0.769 (1.00) |
0.678 (1.00) |
0.403 (1.00) |
0.0752 (1.00) |
1 (1.00) |
0.8 (1.00) |
|
MIRSEQ CNMF |
0.144 (1.00) |
0.0899 (1.00) |
0.763 (1.00) |
0.606 (1.00) |
0.459 (1.00) |
0.366 (1.00) |
0.571 (1.00) |
|
MIRSEQ CHIERARCHICAL |
0.479 (1.00) |
0.854 (1.00) |
1 (1.00) |
0.403 (1.00) |
0.442 (1.00) |
0.716 (1.00) |
0.449 (1.00) |
|
MIRseq Mature CNMF subtypes |
0.83 (1.00) |
0.181 (1.00) |
0.921 (1.00) |
0.623 (1.00) |
0.212 (1.00) |
0.78 (1.00) |
0.705 (1.00) |
|
MIRseq Mature cHierClus subtypes |
0.52 (1.00) |
0.186 (1.00) |
0.911 (1.00) |
0.27 (1.00) |
0.416 (1.00) |
0.905 (1.00) |
0.436 (1.00) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 18 | 7 | 17 |
P value = 0.251 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 41 | 7 | 0.1 - 177.0 (5.5) |
subtype1 | 17 | 2 | 0.3 - 78.3 (5.5) |
subtype2 | 7 | 4 | 1.8 - 70.8 (35.6) |
subtype3 | 17 | 1 | 0.1 - 177.0 (2.4) |
P value = 0.687 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 42 | 46.7 (12.2) |
subtype1 | 18 | 48.3 (10.4) |
subtype2 | 7 | 43.6 (9.2) |
subtype3 | 17 | 46.2 (15.2) |
P value = 0.301 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 13 | 29 |
subtype1 | 5 | 13 |
subtype2 | 4 | 3 |
subtype3 | 4 | 13 |
P value = 0.641 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 14 | 20.6 (13.1) |
subtype1 | 3 | 14.0 (5.3) |
subtype2 | 3 | 23.7 (12.1) |
subtype3 | 8 | 21.9 (15.6) |
P value = 0.324 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 23 | 14 |
subtype1 | 12 | 5 |
subtype2 | 4 | 1 |
subtype3 | 7 | 8 |
P value = 0.583 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 |
---|---|---|
ALL | 24 | 14 |
subtype1 | 11 | 6 |
subtype2 | 2 | 3 |
subtype3 | 11 | 5 |
P value = 0.202 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 0.6 (1.0) |
subtype1 | 16 | 0.6 (1.1) |
subtype2 | 5 | 1.2 (1.6) |
subtype3 | 15 | 0.3 (0.6) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 25 | 16 | 7 |
P value = 0.482 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 47 | 10 | 0.1 - 177.0 (6.0) |
subtype1 | 24 | 7 | 0.1 - 177.0 (5.9) |
subtype2 | 16 | 2 | 0.6 - 101.8 (14.3) |
subtype3 | 7 | 1 | 0.7 - 53.1 (2.2) |
P value = 0.979 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 48 | 47.8 (12.9) |
subtype1 | 25 | 47.5 (12.6) |
subtype2 | 16 | 48.4 (14.6) |
subtype3 | 7 | 47.7 (11.6) |
P value = 0.59 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 16 | 32 |
subtype1 | 7 | 18 |
subtype2 | 7 | 9 |
subtype3 | 2 | 5 |
P value = 0.402 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 14 | 20.6 (13.1) |
subtype1 | 8 | 20.4 (13.9) |
subtype2 | 3 | 13.3 (2.9) |
subtype3 | 3 | 28.3 (16.1) |
P value = 0.315 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 29 | 14 |
subtype1 | 15 | 6 |
subtype2 | 11 | 4 |
subtype3 | 3 | 4 |
P value = 0.316 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 |
---|---|---|
ALL | 27 | 17 |
subtype1 | 11 | 11 |
subtype2 | 11 | 4 |
subtype3 | 5 | 2 |
P value = 0.264 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 42 | 1.1 (2.8) |
subtype1 | 22 | 1.8 (3.7) |
subtype2 | 14 | 0.4 (1.1) |
subtype3 | 6 | 0.3 (0.5) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 26 | 10 | 7 |
P value = 0.977 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 42 | 8 | 0.1 - 177.0 (5.9) |
subtype1 | 26 | 4 | 0.1 - 177.0 (2.7) |
subtype2 | 9 | 3 | 1.0 - 101.8 (30.4) |
subtype3 | 7 | 1 | 0.7 - 53.1 (7.9) |
P value = 0.589 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 43 | 46.6 (11.6) |
subtype1 | 26 | 48.1 (12.5) |
subtype2 | 10 | 44.6 (10.6) |
subtype3 | 7 | 44.0 (9.5) |
P value = 0.424 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 14 | 29 |
subtype1 | 7 | 19 |
subtype2 | 5 | 5 |
subtype3 | 2 | 5 |
P value = 0.412 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 14 | 20.6 (13.1) |
subtype1 | 9 | 18.6 (13.1) |
subtype2 | 2 | 18.0 (9.9) |
subtype3 | 3 | 28.3 (16.1) |
P value = 0.0517 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 25 | 13 |
subtype1 | 15 | 9 |
subtype2 | 7 | 0 |
subtype3 | 3 | 4 |
P value = 0.9 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 |
---|---|---|
ALL | 24 | 15 |
subtype1 | 15 | 10 |
subtype2 | 4 | 3 |
subtype3 | 5 | 2 |
P value = 0.18 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 37 | 1.0 (2.7) |
subtype1 | 24 | 0.7 (1.2) |
subtype2 | 7 | 2.7 (5.9) |
subtype3 | 6 | 0.3 (0.5) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 6 | 31 | 6 |
P value = 0.577 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 42 | 8 | 0.1 - 177.0 (5.9) |
subtype1 | 5 | 0 | 1.0 - 101.8 (12.4) |
subtype2 | 31 | 7 | 0.1 - 177.0 (5.5) |
subtype3 | 6 | 1 | 0.7 - 53.1 (5.0) |
P value = 0.769 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 43 | 46.6 (11.6) |
subtype1 | 6 | 49.7 (7.2) |
subtype2 | 31 | 46.4 (12.6) |
subtype3 | 6 | 45.0 (10.0) |
P value = 0.678 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 14 | 29 |
subtype1 | 3 | 3 |
subtype2 | 9 | 22 |
subtype3 | 2 | 4 |
P value = 0.403 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 14 | 20.6 (13.1) |
subtype2 | 11 | 18.5 (12.1) |
subtype3 | 3 | 28.3 (16.1) |
P value = 0.0752 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 25 | 13 |
subtype1 | 5 | 0 |
subtype2 | 18 | 9 |
subtype3 | 2 | 4 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 |
---|---|---|
ALL | 24 | 15 |
subtype1 | 3 | 2 |
subtype2 | 17 | 11 |
subtype3 | 4 | 2 |
P value = 0.8 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 37 | 1.0 (2.7) |
subtype1 | 5 | 0.6 (0.9) |
subtype2 | 27 | 1.2 (3.2) |
subtype3 | 5 | 0.4 (0.5) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 22 | 15 | 3 | 8 |
P value = 0.144 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 47 | 10 | 0.1 - 177.0 (6.0) |
subtype1 | 21 | 5 | 0.3 - 177.0 (5.8) |
subtype2 | 15 | 3 | 0.1 - 95.1 (6.9) |
subtype3 | 3 | 1 | 0.6 - 8.8 (3.5) |
subtype4 | 8 | 1 | 0.7 - 78.3 (5.0) |
P value = 0.0899 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 48 | 47.8 (12.9) |
subtype1 | 22 | 50.8 (13.2) |
subtype2 | 15 | 42.5 (8.9) |
subtype3 | 3 | 59.3 (21.4) |
subtype4 | 8 | 45.5 (12.5) |
P value = 0.763 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 16 | 32 |
subtype1 | 7 | 15 |
subtype2 | 6 | 9 |
subtype3 | 0 | 3 |
subtype4 | 3 | 5 |
P value = 0.606 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 14 | 20.6 (13.1) |
subtype1 | 4 | 18.0 (5.7) |
subtype2 | 6 | 20.2 (16.0) |
subtype3 | 1 | 10.0 (NA) |
subtype4 | 3 | 28.3 (16.1) |
P value = 0.459 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 29 | 14 |
subtype1 | 13 | 7 |
subtype2 | 10 | 2 |
subtype3 | 2 | 1 |
subtype4 | 4 | 4 |
P value = 0.366 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 |
---|---|---|
ALL | 27 | 17 |
subtype1 | 12 | 8 |
subtype2 | 6 | 7 |
subtype3 | 3 | 0 |
subtype4 | 6 | 2 |
P value = 0.571 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 42 | 1.1 (2.8) |
subtype1 | 20 | 1.1 (2.1) |
subtype2 | 12 | 1.9 (4.5) |
subtype3 | 3 | 0.0 (0.0) |
subtype4 | 7 | 0.3 (0.5) |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 39 | 9 |
P value = 0.479 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 47 | 10 | 0.1 - 177.0 (6.0) |
subtype1 | 38 | 8 | 0.1 - 177.0 (6.4) |
subtype2 | 9 | 2 | 0.7 - 53.1 (6.0) |
P value = 0.854 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 48 | 47.8 (12.9) |
subtype1 | 39 | 48.0 (13.6) |
subtype2 | 9 | 47.2 (10.1) |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 16 | 32 |
subtype1 | 13 | 26 |
subtype2 | 3 | 6 |
P value = 0.403 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 14 | 20.6 (13.1) |
subtype1 | 11 | 18.5 (12.1) |
subtype2 | 3 | 28.3 (16.1) |
P value = 0.442 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 29 | 14 |
subtype1 | 24 | 10 |
subtype2 | 5 | 4 |
P value = 0.716 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 |
---|---|---|
ALL | 27 | 17 |
subtype1 | 22 | 13 |
subtype2 | 5 | 4 |
P value = 0.449 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 42 | 1.1 (2.8) |
subtype1 | 34 | 0.8 (1.7) |
subtype2 | 8 | 2.4 (5.5) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 22 | 18 | 8 |
P value = 0.83 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 47 | 10 | 0.1 - 177.0 (6.0) |
subtype1 | 22 | 5 | 0.1 - 177.0 (10.6) |
subtype2 | 17 | 4 | 0.6 - 101.8 (5.5) |
subtype3 | 8 | 1 | 0.7 - 53.1 (2.0) |
P value = 0.181 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 48 | 47.8 (12.9) |
subtype1 | 22 | 46.3 (13.8) |
subtype2 | 18 | 52.0 (12.2) |
subtype3 | 8 | 42.8 (10.2) |
P value = 0.921 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 16 | 32 |
subtype1 | 8 | 14 |
subtype2 | 6 | 12 |
subtype3 | 2 | 6 |
P value = 0.623 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 14 | 20.6 (13.1) |
subtype1 | 6 | 21.0 (15.8) |
subtype2 | 4 | 15.5 (6.7) |
subtype3 | 4 | 25.0 (14.7) |
P value = 0.212 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 29 | 14 |
subtype1 | 15 | 4 |
subtype2 | 11 | 6 |
subtype3 | 3 | 4 |
P value = 0.78 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 |
---|---|---|
ALL | 27 | 17 |
subtype1 | 11 | 8 |
subtype2 | 10 | 7 |
subtype3 | 6 | 2 |
P value = 0.705 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 42 | 1.1 (2.8) |
subtype1 | 18 | 1.3 (3.7) |
subtype2 | 17 | 1.2 (2.2) |
subtype3 | 7 | 0.3 (0.5) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 5 | 18 | 25 |
P value = 0.52 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 47 | 10 | 0.1 - 177.0 (6.0) |
subtype1 | 5 | 1 | 0.7 - 35.6 (2.2) |
subtype2 | 17 | 2 | 0.1 - 95.1 (5.5) |
subtype3 | 25 | 7 | 0.3 - 177.0 (21.7) |
P value = 0.186 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 48 | 47.8 (12.9) |
subtype1 | 5 | 44.2 (11.0) |
subtype2 | 18 | 44.3 (10.2) |
subtype3 | 25 | 51.1 (14.4) |
P value = 0.911 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 16 | 32 |
subtype1 | 1 | 4 |
subtype2 | 6 | 12 |
subtype3 | 9 | 16 |
P value = 0.27 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 14 | 20.6 (13.1) |
subtype1 | 2 | 37.5 (3.5) |
subtype2 | 6 | 21.8 (15.9) |
subtype3 | 6 | 13.7 (3.8) |
P value = 0.416 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 29 | 14 |
subtype1 | 2 | 3 |
subtype2 | 10 | 4 |
subtype3 | 17 | 7 |
P value = 0.905 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 |
---|---|---|
ALL | 27 | 17 |
subtype1 | 3 | 2 |
subtype2 | 10 | 5 |
subtype3 | 14 | 10 |
P value = 0.436 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 42 | 1.1 (2.8) |
subtype1 | 4 | 0.5 (0.6) |
subtype2 | 15 | 0.5 (0.7) |
subtype3 | 23 | 1.6 (3.7) |
-
Cluster data file = CESC-TP.mergedcluster.txt
-
Clinical data file = CESC-TP.clin.merged.picked.txt
-
Number of patients = 48
-
Number of clustering approaches = 8
-
Number of selected clinical features = 8
-
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
For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between two tumor subtypes using 't.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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.