(WT 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 8 different clustering approaches and 7 clinical features across 23 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 RPPA data identified 2 subtypes that do not correlate to any clinical features.
-
Consensus hierarchical clustering analysis on RPPA data identified 3 subtypes that 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.
-
2 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 |
Time to Death |
AGE |
PRIMARY SITE OF DISEASE |
GENDER |
LYMPH NODE METASTASIS |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
Statistical Tests | logrank test | ANOVA | Chi-square test | Fisher's exact test | Chi-square test | ANOVA | Chi-square test |
Copy Number Ratio CNMF subtypes |
0.571 (1.00) |
0.0316 (1.00) |
0.163 (1.00) |
0.684 (1.00) |
0.533 (1.00) |
0.352 (1.00) |
|
METHLYATION CNMF |
0.394 (1.00) |
0.0966 (1.00) |
0.315 (1.00) |
0.68 (1.00) |
0.259 (1.00) |
0.352 (1.00) |
|
RPPA CNMF subtypes |
0.378 (1.00) |
0.0509 (1.00) |
0.224 (1.00) |
0.637 (1.00) |
0.332 (1.00) |
0.205 (1.00) |
|
RPPA cHierClus subtypes |
0.716 (1.00) |
0.479 (1.00) |
0.404 (1.00) |
1 (1.00) |
0.393 (1.00) |
0.121 (1.00) |
|
RNAseq CNMF subtypes |
0.362 (1.00) |
0.333 (1.00) |
0.659 (1.00) |
0.392 (1.00) |
0.256 (1.00) |
||
RNAseq cHierClus subtypes |
0.968 (1.00) |
0.558 (1.00) |
1 (1.00) |
0.274 (1.00) |
0.165 (1.00) |
||
MIRSEQ CNMF |
0.114 (1.00) |
0.211 (1.00) |
0.0382 (1.00) |
1 (1.00) |
0.259 (1.00) |
0.324 (1.00) |
|
MIRSEQ CHIERARCHICAL |
0.679 (1.00) |
0.223 (1.00) |
0.0979 (1.00) |
0.337 (1.00) |
0.7 (1.00) |
0.285 (1.00) |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 12 | 11 |
P value = 0.571 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 14 | 9 | 4.9 - 78.4 (13.8) |
subtype1 | 8 | 5 | 4.9 - 45.7 (10.7) |
subtype2 | 6 | 4 | 12.2 - 78.4 (17.4) |
P value = 0.0316 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 23 | 59.4 (13.1) |
subtype1 | 12 | 64.9 (13.1) |
subtype2 | 11 | 53.5 (10.7) |
P value = 0.163 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 3 | 6 | 14 |
subtype1 | 3 | 2 | 7 |
subtype2 | 0 | 4 | 7 |
P value = 0.684 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 12 | 11 |
subtype1 | 7 | 5 |
subtype2 | 5 | 6 |
P value = 0.533 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2B | N3 |
---|---|---|---|---|---|---|
ALL | 11 | 1 | 2 | 3 | 2 | 2 |
subtype1 | 7 | 0 | 1 | 2 | 1 | 0 |
subtype2 | 4 | 1 | 1 | 1 | 1 | 2 |
P value = 0.352 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|
ALL | 4 | 1 | 1 | 2 | 3 | 1 | 2 | 2 | 4 |
subtype1 | 1 | 0 | 1 | 2 | 3 | 0 | 1 | 1 | 2 |
subtype2 | 3 | 1 | 0 | 0 | 0 | 1 | 1 | 1 | 2 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 14 | 9 |
P value = 0.394 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 14 | 9 | 4.9 - 78.4 (13.8) |
subtype1 | 9 | 6 | 4.9 - 45.7 (11.2) |
subtype2 | 5 | 3 | 12.2 - 78.4 (19.4) |
P value = 0.0966 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 23 | 59.4 (13.1) |
subtype1 | 14 | 62.8 (14.5) |
subtype2 | 9 | 54.2 (9.1) |
P value = 0.315 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 3 | 6 | 14 |
subtype1 | 3 | 3 | 8 |
subtype2 | 0 | 3 | 6 |
P value = 0.68 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 12 | 11 |
subtype1 | 8 | 6 |
subtype2 | 4 | 5 |
P value = 0.259 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2B | N3 |
---|---|---|---|---|---|---|
ALL | 11 | 1 | 2 | 3 | 2 | 2 |
subtype1 | 7 | 0 | 1 | 3 | 1 | 0 |
subtype2 | 4 | 1 | 1 | 0 | 1 | 2 |
P value = 0.352 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|
ALL | 4 | 1 | 1 | 2 | 3 | 1 | 2 | 2 | 4 |
subtype1 | 1 | 0 | 1 | 2 | 3 | 0 | 1 | 1 | 2 |
subtype2 | 3 | 1 | 0 | 0 | 0 | 1 | 1 | 1 | 2 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 10 | 7 |
P value = 0.378 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 8 | 6 | 4.9 - 78.4 (13.8) |
subtype1 | 5 | 3 | 4.9 - 78.4 (14.7) |
subtype2 | 3 | 3 | 12.2 - 15.3 (13.0) |
P value = 0.0509 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 17 | 57.3 (13.3) |
subtype1 | 10 | 62.5 (12.1) |
subtype2 | 7 | 49.9 (11.9) |
P value = 0.224 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 3 | 3 | 11 |
subtype1 | 3 | 1 | 6 |
subtype2 | 0 | 2 | 5 |
P value = 0.637 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 9 | 8 |
subtype1 | 6 | 4 |
subtype2 | 3 | 4 |
P value = 0.332 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2B | N3 |
---|---|---|---|---|---|---|
ALL | 9 | 1 | 1 | 2 | 1 | 1 |
subtype1 | 5 | 0 | 0 | 2 | 1 | 1 |
subtype2 | 4 | 1 | 1 | 0 | 0 | 0 |
P value = 0.205 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|
ALL | 4 | 1 | 1 | 1 | 2 | 1 | 1 | 1 | 2 |
subtype1 | 1 | 0 | 1 | 1 | 2 | 0 | 0 | 1 | 2 |
subtype2 | 3 | 1 | 0 | 0 | 0 | 1 | 1 | 0 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 6 | 5 | 6 |
P value = 0.716 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 8 | 6 | 4.9 - 78.4 (13.8) |
subtype1 | 2 | 2 | 12.2 - 15.3 (13.8) |
subtype2 | 3 | 2 | 13.0 - 31.3 (14.7) |
subtype3 | 3 | 2 | 4.9 - 78.4 (10.3) |
P value = 0.479 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 17 | 57.3 (13.3) |
subtype1 | 6 | 52.3 (10.8) |
subtype2 | 5 | 62.4 (16.3) |
subtype3 | 6 | 58.0 (13.3) |
P value = 0.404 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 3 | 3 | 11 |
subtype1 | 0 | 2 | 4 |
subtype2 | 1 | 0 | 4 |
subtype3 | 2 | 1 | 3 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 9 | 8 |
subtype1 | 3 | 3 |
subtype2 | 3 | 2 |
subtype3 | 3 | 3 |
P value = 0.393 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2B | N3 |
---|---|---|---|---|---|---|
ALL | 9 | 1 | 1 | 2 | 1 | 1 |
subtype1 | 4 | 1 | 1 | 0 | 0 | 0 |
subtype2 | 3 | 0 | 0 | 0 | 0 | 0 |
subtype3 | 2 | 0 | 0 | 2 | 1 | 1 |
P value = 0.121 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|
ALL | 4 | 1 | 1 | 1 | 2 | 1 | 1 | 1 | 2 |
subtype1 | 3 | 1 | 0 | 0 | 0 | 1 | 1 | 0 | 0 |
subtype2 | 1 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 |
subtype3 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 1 | 2 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 7 | 14 |
P value = 0.362 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 21 | 59.4 (13.7) |
subtype1 | 7 | 56.0 (9.7) |
subtype2 | 14 | 61.1 (15.4) |
P value = 0.333 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 3 | 4 | 14 |
subtype1 | 0 | 1 | 6 |
subtype2 | 3 | 3 | 8 |
P value = 0.659 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 11 | 10 |
subtype1 | 3 | 4 |
subtype2 | 8 | 6 |
P value = 0.392 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2B | N3 |
---|---|---|---|---|---|---|
ALL | 11 | 1 | 1 | 3 | 1 | 2 |
subtype1 | 4 | 0 | 0 | 1 | 0 | 2 |
subtype2 | 7 | 1 | 1 | 2 | 1 | 0 |
P value = 0.256 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|
ALL | 4 | 1 | 1 | 2 | 3 | 1 | 1 | 1 | 4 |
subtype1 | 3 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 2 |
subtype2 | 1 | 0 | 1 | 2 | 3 | 1 | 1 | 1 | 2 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 3 | 6 | 12 |
P value = 0.968 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 21 | 59.4 (13.7) |
subtype1 | 3 | 58.0 (17.1) |
subtype2 | 6 | 58.8 (6.7) |
subtype3 | 12 | 60.1 (16.3) |
P value = 0.558 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 3 | 4 | 14 |
subtype1 | 0 | 1 | 2 |
subtype2 | 0 | 1 | 5 |
subtype3 | 3 | 2 | 7 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 11 | 10 |
subtype1 | 2 | 1 |
subtype2 | 3 | 3 |
subtype3 | 6 | 6 |
P value = 0.274 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2B | N3 |
---|---|---|---|---|---|---|
ALL | 11 | 1 | 1 | 3 | 1 | 2 |
subtype1 | 2 | 0 | 1 | 0 | 0 | 0 |
subtype2 | 3 | 0 | 0 | 1 | 0 | 2 |
subtype3 | 6 | 1 | 0 | 2 | 1 | 0 |
P value = 0.165 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|
ALL | 4 | 1 | 1 | 2 | 3 | 1 | 1 | 1 | 4 |
subtype1 | 0 | 1 | 0 | 0 | 1 | 0 | 1 | 0 | 0 |
subtype2 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 |
subtype3 | 1 | 0 | 1 | 2 | 2 | 1 | 0 | 1 | 2 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 13 | 10 |
P value = 0.114 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 14 | 9 | 4.9 - 78.4 (13.8) |
subtype1 | 7 | 6 | 4.9 - 31.3 (11.2) |
subtype2 | 7 | 3 | 6.6 - 78.4 (15.3) |
P value = 0.211 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 23 | 59.4 (13.1) |
subtype1 | 13 | 62.4 (14.4) |
subtype2 | 10 | 55.6 (10.8) |
P value = 0.0382 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 3 | 6 | 14 |
subtype1 | 3 | 1 | 9 |
subtype2 | 0 | 5 | 5 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 12 | 11 |
subtype1 | 7 | 6 |
subtype2 | 5 | 5 |
P value = 0.259 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2B | N3 |
---|---|---|---|---|---|---|
ALL | 11 | 1 | 2 | 3 | 2 | 2 |
subtype1 | 7 | 0 | 0 | 3 | 1 | 1 |
subtype2 | 4 | 1 | 2 | 0 | 1 | 1 |
P value = 0.324 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|
ALL | 4 | 1 | 1 | 2 | 3 | 1 | 2 | 2 | 4 |
subtype1 | 1 | 1 | 1 | 2 | 2 | 0 | 0 | 1 | 3 |
subtype2 | 3 | 0 | 0 | 0 | 1 | 1 | 2 | 1 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 8 | 7 | 8 |
P value = 0.679 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 14 | 9 | 4.9 - 78.4 (13.8) |
subtype1 | 5 | 3 | 12.2 - 78.4 (15.3) |
subtype2 | 4 | 3 | 6.3 - 31.3 (8.9) |
subtype3 | 5 | 3 | 4.9 - 45.7 (14.7) |
P value = 0.223 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 23 | 59.4 (13.1) |
subtype1 | 8 | 52.9 (10.3) |
subtype2 | 7 | 63.1 (15.0) |
subtype3 | 8 | 62.8 (12.9) |
P value = 0.0979 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 3 | 6 | 14 |
subtype1 | 0 | 3 | 5 |
subtype2 | 0 | 1 | 6 |
subtype3 | 3 | 2 | 3 |
P value = 0.337 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 12 | 11 |
subtype1 | 3 | 5 |
subtype2 | 3 | 4 |
subtype3 | 6 | 2 |
P value = 0.7 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2B | N3 |
---|---|---|---|---|---|---|
ALL | 11 | 1 | 2 | 3 | 2 | 2 |
subtype1 | 3 | 1 | 1 | 0 | 1 | 1 |
subtype2 | 3 | 0 | 1 | 1 | 1 | 0 |
subtype3 | 5 | 0 | 0 | 2 | 0 | 1 |
P value = 0.285 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|
ALL | 4 | 1 | 1 | 2 | 3 | 1 | 2 | 2 | 4 |
subtype1 | 3 | 0 | 0 | 0 | 0 | 1 | 1 | 1 | 1 |
subtype2 | 1 | 1 | 0 | 1 | 0 | 0 | 1 | 0 | 2 |
subtype3 | 0 | 0 | 1 | 1 | 3 | 0 | 0 | 1 | 1 |
-
Cluster data file = SKCM-WT.mergedcluster.txt
-
Clinical data file = SKCM-WT.clin.merged.picked.txt
-
Number of patients = 23
-
Number of clustering approaches = 8
-
Number of selected clinical features = 7
-
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, 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 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 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 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.