(primary solid tumor cohort)
This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 6 different clustering approaches and 10 clinical features across 40 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.
-
3 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes do not correlate to any clinical features.
-
3 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 3 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.
-
3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes do not correlate to any clinical features.
-
3 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes do not correlate to any clinical features.
Clinical Features |
Statistical Tests |
Copy Number Ratio CNMF subtypes |
METHLYATION CNMF |
RNAseq CNMF subtypes |
RNAseq cHierClus subtypes |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
Time to Death | logrank test |
0.514 (1.00) |
0.417 (1.00) |
0.867 (1.00) |
0.557 (1.00) |
0.821 (1.00) |
0.954 (1.00) |
AGE | ANOVA |
0.822 (1.00) |
0.844 (1.00) |
0.413 (1.00) |
0.864 (1.00) |
0.302 (1.00) |
0.215 (1.00) |
HISTOLOGICAL TYPE | Chi-square test |
0.461 (1.00) |
0.0459 (1.00) |
0.0525 (1.00) |
0.0692 (1.00) |
0.669 (1.00) |
0.113 (1.00) |
RADIATIONS RADIATION REGIMENINDICATION | Fisher's exact test |
0.464 (1.00) |
1 (1.00) |
0.161 (1.00) |
0.549 (1.00) |
0.505 (1.00) |
0.531 (1.00) |
NUMBERPACKYEARSSMOKED | ANOVA |
0.636 (1.00) |
0.245 (1.00) |
0.277 (1.00) |
0.72 (1.00) |
0.232 (1.00) |
|
TOBACCOSMOKINGHISTORYINDICATOR | ANOVA |
0.461 (1.00) |
0.629 (1.00) |
0.614 (1.00) |
0.0979 (1.00) |
0.69 (1.00) |
0.594 (1.00) |
DISTANT METASTASIS | Fisher's exact test |
0.525 (1.00) |
0.0565 (1.00) |
0.0558 (1.00) |
0.0461 (1.00) |
0.382 (1.00) |
0.209 (1.00) |
LYMPH NODE METASTASIS | Fisher's exact test |
0.561 (1.00) |
0.149 (1.00) |
1 (1.00) |
0.855 (1.00) |
1 (1.00) |
0.569 (1.00) |
NUMBER OF LYMPH NODES | ANOVA |
0.399 (1.00) |
0.252 (1.00) |
0.196 (1.00) |
0.885 (1.00) |
0.666 (1.00) |
0.554 (1.00) |
TUMOR STAGECODE | ANOVA |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 17 | 5 | 12 |
P value = 0.514 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 33 | 6 | 0.1 - 177.0 (5.8) |
subtype1 | 16 | 2 | 0.3 - 78.3 (5.7) |
subtype2 | 5 | 3 | 5.5 - 70.8 (40.9) |
subtype3 | 12 | 1 | 0.1 - 177.0 (2.3) |
P value = 0.822 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 34 | 47.8 (12.9) |
subtype1 | 17 | 48.2 (10.7) |
subtype2 | 5 | 44.4 (11.1) |
subtype3 | 12 | 48.7 (16.8) |
P value = 0.461 (Chi-square test), Q value = 1
nPatients | CERVICAL SQUAMOUS CELL CARCINOMA | ENDOCERVICAL TYPE OF ADENOCARCINOMA | SQUAMOUS CELL CARCINOMA |
---|---|---|---|
ALL | 27 | 1 | 6 |
subtype1 | 14 | 0 | 3 |
subtype2 | 5 | 0 | 0 |
subtype3 | 8 | 1 | 3 |
P value = 0.464 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 11 | 23 |
subtype1 | 5 | 12 |
subtype2 | 3 | 2 |
subtype3 | 3 | 9 |
P value = 0.636 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 10 | 18.8 (11.3) |
subtype1 | 3 | 14.0 (5.3) |
subtype2 | 3 | 23.7 (12.1) |
subtype3 | 4 | 18.8 (14.9) |
P value = 0.461 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 33 | 1.8 (1.1) |
subtype1 | 16 | 2.1 (1.3) |
subtype2 | 5 | 1.6 (0.5) |
subtype3 | 12 | 1.6 (0.9) |
P value = 0.525 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 20 | 9 |
subtype1 | 11 | 5 |
subtype2 | 3 | 0 |
subtype3 | 6 | 4 |
P value = 0.561 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 |
---|---|---|
ALL | 19 | 11 |
subtype1 | 10 | 6 |
subtype2 | 1 | 2 |
subtype3 | 8 | 3 |
P value = 0.399 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 30 | 0.5 (0.9) |
subtype1 | 16 | 0.6 (1.1) |
subtype2 | 3 | 0.7 (0.6) |
subtype3 | 11 | 0.2 (0.4) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 24 | 12 | 4 |
P value = 0.417 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 39 | 9 | 0.1 - 177.0 (6.9) |
subtype1 | 23 | 7 | 0.1 - 177.0 (6.0) |
subtype2 | 12 | 2 | 0.6 - 101.8 (27.9) |
subtype3 | 4 | 0 | 1.0 - 53.1 (1.7) |
P value = 0.844 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 40 | 49.0 (13.5) |
subtype1 | 24 | 48.1 (13.2) |
subtype2 | 12 | 50.9 (14.5) |
subtype3 | 4 | 49.0 (15.3) |
P value = 0.0459 (Chi-square test), Q value = 1
nPatients | CERVICAL SQUAMOUS CELL CARCINOMA | ENDOCERVICAL TYPE OF ADENOCARCINOMA | SQUAMOUS CELL CARCINOMA |
---|---|---|---|
ALL | 33 | 1 | 6 |
subtype1 | 20 | 0 | 4 |
subtype2 | 10 | 0 | 2 |
subtype3 | 3 | 1 | 0 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 15 | 25 |
subtype1 | 9 | 15 |
subtype2 | 5 | 7 |
subtype3 | 1 | 3 |
P value = 0.629 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 37 | 1.9 (1.1) |
subtype1 | 22 | 2.0 (1.2) |
subtype2 | 11 | 1.6 (0.9) |
subtype3 | 4 | 2.0 (1.4) |
P value = 0.0565 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 26 | 9 |
subtype1 | 15 | 5 |
subtype2 | 10 | 1 |
subtype3 | 1 | 3 |
P value = 0.149 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 |
---|---|---|
ALL | 22 | 14 |
subtype1 | 10 | 11 |
subtype2 | 9 | 2 |
subtype3 | 3 | 1 |
P value = 0.252 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 1.1 (3.0) |
subtype1 | 21 | 1.8 (3.7) |
subtype2 | 11 | 0.1 (0.3) |
subtype3 | 4 | 0.2 (0.5) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 21 | 10 | 5 |
P value = 0.867 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 35 | 7 | 0.1 - 177.0 (6.0) |
subtype1 | 21 | 3 | 0.1 - 177.0 (2.7) |
subtype2 | 9 | 3 | 1.0 - 101.8 (30.4) |
subtype3 | 5 | 1 | 1.2 - 53.1 (25.4) |
P value = 0.413 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 47.6 (12.0) |
subtype1 | 21 | 49.9 (12.8) |
subtype2 | 10 | 44.6 (10.6) |
subtype3 | 5 | 44.0 (10.9) |
P value = 0.0525 (Chi-square test), Q value = 1
nPatients | CERVICAL SQUAMOUS CELL CARCINOMA | ENDOCERVICAL TYPE OF ADENOCARCINOMA | SQUAMOUS CELL CARCINOMA |
---|---|---|---|
ALL | 31 | 1 | 4 |
subtype1 | 17 | 0 | 4 |
subtype2 | 10 | 0 | 0 |
subtype3 | 4 | 1 | 0 |
P value = 0.161 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 13 | 23 |
subtype1 | 5 | 16 |
subtype2 | 6 | 4 |
subtype3 | 2 | 3 |
P value = 0.245 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 10 | 18.8 (11.3) |
subtype1 | 5 | 13.4 (5.5) |
subtype2 | 2 | 18.0 (9.9) |
subtype3 | 3 | 28.3 (16.1) |
P value = 0.614 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 33 | 1.9 (1.1) |
subtype1 | 20 | 1.8 (1.1) |
subtype2 | 8 | 2.1 (1.2) |
subtype3 | 5 | 2.2 (1.1) |
P value = 0.0558 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 23 | 8 |
subtype1 | 14 | 5 |
subtype2 | 7 | 0 |
subtype3 | 2 | 3 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 |
---|---|---|
ALL | 20 | 12 |
subtype1 | 13 | 7 |
subtype2 | 4 | 3 |
subtype3 | 3 | 2 |
P value = 0.196 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 32 | 1.0 (2.9) |
subtype1 | 20 | 0.5 (1.0) |
subtype2 | 7 | 2.7 (5.9) |
subtype3 | 5 | 0.4 (0.5) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 6 | 26 | 4 |
P value = 0.557 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 35 | 7 | 0.1 - 177.0 (6.0) |
subtype1 | 5 | 0 | 1.0 - 101.8 (12.4) |
subtype2 | 26 | 6 | 0.1 - 177.0 (5.7) |
subtype3 | 4 | 1 | 1.2 - 53.1 (18.9) |
P value = 0.864 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 47.6 (12.0) |
subtype1 | 6 | 49.7 (7.2) |
subtype2 | 26 | 47.4 (13.1) |
subtype3 | 4 | 45.5 (12.0) |
P value = 0.0692 (Chi-square test), Q value = 1
nPatients | CERVICAL SQUAMOUS CELL CARCINOMA | ENDOCERVICAL TYPE OF ADENOCARCINOMA | SQUAMOUS CELL CARCINOMA |
---|---|---|---|
ALL | 31 | 1 | 4 |
subtype1 | 5 | 0 | 1 |
subtype2 | 23 | 0 | 3 |
subtype3 | 3 | 1 | 0 |
P value = 0.549 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 13 | 23 |
subtype1 | 3 | 3 |
subtype2 | 8 | 18 |
subtype3 | 2 | 2 |
P value = 0.277 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 10 | 18.8 (11.3) |
subtype2 | 7 | 14.7 (6.4) |
subtype3 | 3 | 28.3 (16.1) |
P value = 0.0979 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 33 | 1.9 (1.1) |
subtype1 | 5 | 2.8 (1.3) |
subtype2 | 24 | 1.7 (1.0) |
subtype3 | 4 | 2.2 (1.3) |
P value = 0.0461 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 23 | 8 |
subtype1 | 5 | 0 |
subtype2 | 17 | 5 |
subtype3 | 1 | 3 |
P value = 0.855 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 |
---|---|---|
ALL | 20 | 12 |
subtype1 | 3 | 2 |
subtype2 | 15 | 8 |
subtype3 | 2 | 2 |
P value = 0.885 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 32 | 1.0 (2.9) |
subtype1 | 5 | 0.6 (0.9) |
subtype2 | 23 | 1.1 (3.4) |
subtype3 | 4 | 0.5 (0.6) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 15 | 15 | 10 |
P value = 0.821 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 39 | 9 | 0.1 - 177.0 (6.9) |
subtype1 | 15 | 5 | 0.1 - 177.0 (12.4) |
subtype2 | 14 | 3 | 0.6 - 101.8 (15.5) |
subtype3 | 10 | 1 | 1.0 - 78.3 (4.3) |
P value = 0.302 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 40 | 49.0 (13.5) |
subtype1 | 15 | 47.0 (15.1) |
subtype2 | 15 | 53.3 (11.5) |
subtype3 | 10 | 45.7 (13.2) |
P value = 0.669 (Chi-square test), Q value = 1
nPatients | CERVICAL SQUAMOUS CELL CARCINOMA | ENDOCERVICAL TYPE OF ADENOCARCINOMA | SQUAMOUS CELL CARCINOMA |
---|---|---|---|
ALL | 33 | 1 | 6 |
subtype1 | 13 | 0 | 2 |
subtype2 | 11 | 1 | 3 |
subtype3 | 9 | 0 | 1 |
P value = 0.505 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 15 | 25 |
subtype1 | 6 | 9 |
subtype2 | 4 | 11 |
subtype3 | 5 | 5 |
P value = 0.72 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 10 | 18.8 (11.3) |
subtype1 | 4 | 15.2 (9.0) |
subtype2 | 2 | 27.5 (17.7) |
subtype3 | 4 | 18.0 (11.5) |
P value = 0.69 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 37 | 1.9 (1.1) |
subtype1 | 14 | 1.7 (1.1) |
subtype2 | 14 | 2.0 (1.2) |
subtype3 | 9 | 2.1 (1.3) |
P value = 0.382 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 26 | 9 |
subtype1 | 10 | 2 |
subtype2 | 11 | 3 |
subtype3 | 5 | 4 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 |
---|---|---|
ALL | 22 | 14 |
subtype1 | 7 | 5 |
subtype2 | 9 | 5 |
subtype3 | 6 | 4 |
P value = 0.666 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 1.1 (3.0) |
subtype1 | 12 | 1.8 (4.5) |
subtype2 | 14 | 0.9 (2.1) |
subtype3 | 10 | 0.7 (1.3) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 5 | 22 | 13 |
P value = 0.954 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 39 | 9 | 0.1 - 177.0 (6.9) |
subtype1 | 5 | 1 | 1.2 - 53.1 (6.0) |
subtype2 | 22 | 6 | 0.3 - 177.0 (17.1) |
subtype3 | 12 | 2 | 0.1 - 95.1 (6.2) |
P value = 0.215 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 40 | 49.0 (13.5) |
subtype1 | 5 | 45.6 (10.4) |
subtype2 | 22 | 52.4 (14.8) |
subtype3 | 13 | 44.6 (11.0) |
P value = 0.113 (Chi-square test), Q value = 1
nPatients | CERVICAL SQUAMOUS CELL CARCINOMA | ENDOCERVICAL TYPE OF ADENOCARCINOMA | SQUAMOUS CELL CARCINOMA |
---|---|---|---|
ALL | 33 | 1 | 6 |
subtype1 | 3 | 1 | 1 |
subtype2 | 19 | 0 | 3 |
subtype3 | 11 | 0 | 2 |
P value = 0.531 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 15 | 25 |
subtype1 | 3 | 2 |
subtype2 | 8 | 14 |
subtype3 | 4 | 9 |
P value = 0.232 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 10 | 18.8 (11.3) |
subtype1 | 3 | 28.3 (16.1) |
subtype2 | 3 | 15.7 (4.0) |
subtype3 | 4 | 14.0 (8.4) |
P value = 0.594 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 37 | 1.9 (1.1) |
subtype1 | 5 | 2.4 (1.1) |
subtype2 | 21 | 1.8 (1.2) |
subtype3 | 11 | 1.9 (1.1) |
P value = 0.209 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 26 | 9 |
subtype1 | 2 | 3 |
subtype2 | 17 | 4 |
subtype3 | 7 | 2 |
P value = 0.569 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 |
---|---|---|
ALL | 22 | 14 |
subtype1 | 2 | 3 |
subtype2 | 13 | 8 |
subtype3 | 7 | 3 |
P value = 0.554 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 1.1 (3.0) |
subtype1 | 5 | 0.6 (0.5) |
subtype2 | 21 | 1.6 (3.8) |
subtype3 | 10 | 0.4 (0.7) |
-
Cluster data file = CESC-TP.mergedcluster.txt
-
Clinical data file = CESC-TP.clin.merged.picked.txt
-
Number of patients = 40
-
Number of clustering approaches = 6
-
Number of selected clinical features = 10
-
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 multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.