This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 10 different clustering approaches and 8 clinical features across 36 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.
-
3 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 4 subtypes that 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 6 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.
-
6 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 |
YEARS TO BIRTH |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER | RACE |
Statistical Tests | logrank test | Kruskal-Wallis (anova) | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test |
Copy Number Ratio CNMF subtypes |
0.481 (1.00) |
0.849 (1.00) |
0.645 (1.00) |
1 (1.00) |
0.344 (1.00) |
1 (1.00) |
0.749 (1.00) |
0.229 (1.00) |
METHLYATION CNMF |
0.872 (1.00) |
0.235 (1.00) |
0.224 (1.00) |
0.752 (1.00) |
0.587 (1.00) |
0.589 (1.00) |
0.635 (1.00) |
0.702 (1.00) |
RPPA CNMF subtypes |
0.661 (1.00) |
0.377 (1.00) |
0.673 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
RPPA cHierClus subtypes |
0.473 (1.00) |
0.0524 (1.00) |
0.471 (1.00) |
0.398 (1.00) |
0.285 (1.00) |
0.149 (1.00) |
0.695 (1.00) |
0.606 (1.00) |
RNAseq CNMF subtypes |
0.905 (1.00) |
0.495 (1.00) |
0.654 (1.00) |
0.612 (1.00) |
0.568 (1.00) |
1 (1.00) |
0.0559 (1.00) |
0.481 (1.00) |
RNAseq cHierClus subtypes |
0.263 (1.00) |
0.376 (1.00) |
0.412 (1.00) |
0.722 (1.00) |
0.0138 (1.00) |
0.239 (1.00) |
0.146 (1.00) |
0.358 (1.00) |
MIRSEQ CNMF |
0.65 (1.00) |
0.433 (1.00) |
0.5 (1.00) |
0.681 (1.00) |
0.594 (1.00) |
0.229 (1.00) |
0.937 (1.00) |
0.712 (1.00) |
MIRSEQ CHIERARCHICAL |
0.984 (1.00) |
0.986 (1.00) |
0.705 (1.00) |
0.905 (1.00) |
1 (1.00) |
0.87 (1.00) |
0.0504 (1.00) |
0.467 (1.00) |
MIRseq Mature CNMF subtypes |
0.518 (1.00) |
0.607 (1.00) |
0.98 (1.00) |
0.585 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.777 (1.00) |
MIRseq Mature cHierClus subtypes |
0.675 (1.00) |
0.174 (1.00) |
0.967 (1.00) |
0.909 (1.00) |
0.983 (1.00) |
0.563 (1.00) |
0.556 (1.00) |
0.714 (1.00) |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 19 | 17 |
P value = 0.481 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 36 | 18 | 0.3 - 65.0 (18.1) |
subtype1 | 19 | 7 | 0.3 - 65.0 (13.2) |
subtype2 | 17 | 11 | 0.7 - 63.8 (20.6) |
P value = 0.849 (Wilcoxon-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 63.0 (12.9) |
subtype1 | 19 | 63.1 (12.3) |
subtype2 | 17 | 62.9 (13.8) |
P value = 0.645 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|
ALL | 19 | 9 | 1 | 2 | 2 | 3 |
subtype1 | 10 | 3 | 1 | 1 | 2 | 2 |
subtype2 | 9 | 6 | 0 | 1 | 0 | 1 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 19 | 12 | 5 |
subtype1 | 10 | 6 | 3 |
subtype2 | 9 | 6 | 2 |
P value = 0.344 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 26 | 5 |
subtype1 | 13 | 4 |
subtype2 | 13 | 1 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 28 | 5 |
subtype1 | 15 | 3 |
subtype2 | 13 | 2 |
P value = 0.749 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 20 | 16 |
subtype1 | 10 | 9 |
subtype2 | 10 | 7 |
P value = 0.229 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 2 | 31 |
subtype1 | 3 | 1 | 15 |
subtype2 | 0 | 1 | 16 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 13 | 10 | 13 |
P value = 0.872 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 36 | 18 | 0.3 - 65.0 (18.1) |
subtype1 | 13 | 4 | 0.3 - 48.8 (13.2) |
subtype2 | 10 | 7 | 0.8 - 65.0 (19.6) |
subtype3 | 13 | 7 | 1.6 - 63.8 (20.6) |
P value = 0.235 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 63.0 (12.9) |
subtype1 | 13 | 65.8 (10.2) |
subtype2 | 10 | 58.8 (11.2) |
subtype3 | 13 | 63.5 (16.2) |
P value = 0.224 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|
ALL | 19 | 9 | 1 | 2 | 2 | 3 |
subtype1 | 8 | 2 | 1 | 0 | 0 | 2 |
subtype2 | 6 | 2 | 0 | 2 | 0 | 0 |
subtype3 | 5 | 5 | 0 | 0 | 2 | 1 |
P value = 0.752 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 19 | 12 | 5 |
subtype1 | 8 | 3 | 2 |
subtype2 | 6 | 3 | 1 |
subtype3 | 5 | 6 | 2 |
P value = 0.587 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 26 | 5 |
subtype1 | 9 | 2 |
subtype2 | 7 | 0 |
subtype3 | 10 | 3 |
P value = 0.589 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 28 | 5 |
subtype1 | 9 | 2 |
subtype2 | 7 | 2 |
subtype3 | 12 | 1 |
P value = 0.635 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 20 | 16 |
subtype1 | 6 | 7 |
subtype2 | 7 | 3 |
subtype3 | 7 | 6 |
P value = 0.702 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 2 | 31 |
subtype1 | 2 | 1 | 10 |
subtype2 | 0 | 1 | 9 |
subtype3 | 1 | 0 | 12 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 11 | 19 |
P value = 0.661 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 30 | 15 | 0.3 - 65.0 (18.1) |
subtype1 | 11 | 5 | 5.6 - 65.0 (17.1) |
subtype2 | 19 | 10 | 0.3 - 63.8 (20.6) |
P value = 0.377 (Wilcoxon-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 30 | 63.1 (13.8) |
subtype1 | 11 | 66.2 (12.1) |
subtype2 | 19 | 61.4 (14.7) |
P value = 0.673 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|
ALL | 17 | 6 | 1 | 2 | 2 | 2 |
subtype1 | 7 | 2 | 1 | 0 | 0 | 1 |
subtype2 | 10 | 4 | 0 | 2 | 2 | 1 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 17 | 9 | 4 |
subtype1 | 7 | 3 | 1 |
subtype2 | 10 | 6 | 3 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 22 | 4 |
subtype1 | 9 | 1 |
subtype2 | 13 | 3 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 24 | 4 |
subtype1 | 10 | 1 |
subtype2 | 14 | 3 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 17 | 13 |
subtype1 | 6 | 5 |
subtype2 | 11 | 8 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 2 | 2 | 26 |
subtype1 | 1 | 1 | 9 |
subtype2 | 1 | 1 | 17 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 6 | 7 | 8 | 9 |
P value = 0.473 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 30 | 15 | 0.3 - 65.0 (18.1) |
subtype1 | 6 | 5 | 8.9 - 63.8 (15.5) |
subtype2 | 7 | 2 | 5.6 - 65.0 (17.1) |
subtype3 | 8 | 4 | 0.7 - 35.5 (21.8) |
subtype4 | 9 | 4 | 0.3 - 46.1 (18.1) |
P value = 0.0524 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 30 | 63.1 (13.8) |
subtype1 | 6 | 70.7 (3.7) |
subtype2 | 7 | 63.4 (14.6) |
subtype3 | 8 | 69.0 (9.4) |
subtype4 | 9 | 52.7 (15.5) |
P value = 0.471 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|
ALL | 17 | 6 | 1 | 2 | 2 | 2 |
subtype1 | 3 | 0 | 1 | 0 | 1 | 1 |
subtype2 | 5 | 2 | 0 | 0 | 0 | 0 |
subtype3 | 6 | 2 | 0 | 0 | 0 | 0 |
subtype4 | 3 | 2 | 0 | 2 | 1 | 1 |
P value = 0.398 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 17 | 9 | 4 |
subtype1 | 3 | 1 | 2 |
subtype2 | 5 | 2 | 0 |
subtype3 | 6 | 2 | 0 |
subtype4 | 3 | 4 | 2 |
P value = 0.285 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 22 | 4 |
subtype1 | 4 | 2 |
subtype2 | 6 | 0 |
subtype3 | 6 | 0 |
subtype4 | 6 | 2 |
P value = 0.149 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 24 | 4 |
subtype1 | 5 | 1 |
subtype2 | 7 | 0 |
subtype3 | 7 | 0 |
subtype4 | 5 | 3 |
P value = 0.695 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 17 | 13 |
subtype1 | 3 | 3 |
subtype2 | 4 | 3 |
subtype3 | 6 | 2 |
subtype4 | 4 | 5 |
P value = 0.606 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 2 | 2 | 26 |
subtype1 | 1 | 0 | 5 |
subtype2 | 0 | 1 | 6 |
subtype3 | 1 | 1 | 6 |
subtype4 | 0 | 0 | 9 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 12 | 15 | 9 |
P value = 0.905 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 36 | 18 | 0.3 - 65.0 (18.1) |
subtype1 | 12 | 5 | 8.9 - 48.8 (16.3) |
subtype2 | 15 | 8 | 1.6 - 63.8 (20.0) |
subtype3 | 9 | 5 | 0.3 - 65.0 (13.4) |
P value = 0.495 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 63.0 (12.9) |
subtype1 | 12 | 66.2 (11.8) |
subtype2 | 15 | 59.2 (15.1) |
subtype3 | 9 | 65.0 (9.4) |
P value = 0.654 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|
ALL | 19 | 9 | 1 | 2 | 2 | 3 |
subtype1 | 7 | 2 | 1 | 0 | 0 | 2 |
subtype2 | 6 | 5 | 0 | 1 | 2 | 1 |
subtype3 | 6 | 2 | 0 | 1 | 0 | 0 |
P value = 0.612 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 19 | 12 | 5 |
subtype1 | 7 | 3 | 2 |
subtype2 | 6 | 6 | 3 |
subtype3 | 6 | 3 | 0 |
P value = 0.568 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 26 | 5 |
subtype1 | 8 | 2 |
subtype2 | 11 | 3 |
subtype3 | 7 | 0 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 28 | 5 |
subtype1 | 8 | 2 |
subtype2 | 13 | 2 |
subtype3 | 7 | 1 |
P value = 0.0559 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 20 | 16 |
subtype1 | 7 | 5 |
subtype2 | 11 | 4 |
subtype3 | 2 | 7 |
P value = 0.481 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 2 | 31 |
subtype1 | 2 | 0 | 10 |
subtype2 | 1 | 2 | 12 |
subtype3 | 0 | 0 | 9 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
---|---|---|---|---|---|---|---|
Number of samples | 4 | 5 | 5 | 9 | 6 | 5 | 2 |
P value = 0.263 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 34 | 17 | 0.3 - 65.0 (18.1) |
subtype1 | 4 | 3 | 8.9 - 13.2 (12.2) |
subtype2 | 5 | 1 | 10.2 - 48.8 (18.1) |
subtype3 | 5 | 1 | 6.8 - 35.5 (20.6) |
subtype4 | 9 | 5 | 0.3 - 65.0 (13.4) |
subtype5 | 6 | 5 | 5.6 - 63.8 (35.9) |
subtype6 | 5 | 2 | 1.6 - 33.4 (12.7) |
P value = 0.376 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 34 | 64.6 (11.3) |
subtype1 | 4 | 65.0 (9.6) |
subtype2 | 5 | 60.6 (13.1) |
subtype3 | 5 | 73.0 (7.6) |
subtype4 | 9 | 65.0 (9.4) |
subtype5 | 6 | 61.3 (8.0) |
subtype6 | 5 | 63.0 (19.2) |
P value = 0.412 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|
ALL | 18 | 9 | 1 | 2 | 1 | 3 |
subtype1 | 2 | 0 | 0 | 0 | 0 | 2 |
subtype2 | 2 | 2 | 1 | 0 | 0 | 0 |
subtype3 | 4 | 1 | 0 | 0 | 0 | 0 |
subtype4 | 6 | 2 | 0 | 1 | 0 | 0 |
subtype5 | 3 | 2 | 0 | 1 | 0 | 0 |
subtype6 | 1 | 2 | 0 | 0 | 1 | 1 |
P value = 0.722 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 18 | 11 | 5 |
subtype1 | 2 | 1 | 1 |
subtype2 | 2 | 2 | 1 |
subtype3 | 4 | 1 | 0 |
subtype4 | 6 | 3 | 0 |
subtype5 | 3 | 2 | 1 |
subtype6 | 1 | 2 | 2 |
P value = 0.0138 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 25 | 4 |
subtype1 | 1 | 2 |
subtype2 | 4 | 0 |
subtype3 | 5 | 0 |
subtype4 | 7 | 0 |
subtype5 | 5 | 0 |
subtype6 | 3 | 2 |
P value = 0.239 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 26 | 5 |
subtype1 | 1 | 2 |
subtype2 | 4 | 0 |
subtype3 | 5 | 0 |
subtype4 | 7 | 1 |
subtype5 | 5 | 1 |
subtype6 | 4 | 1 |
P value = 0.146 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 18 | 16 |
subtype1 | 1 | 3 |
subtype2 | 4 | 1 |
subtype3 | 3 | 2 |
subtype4 | 2 | 7 |
subtype5 | 5 | 1 |
subtype6 | 3 | 2 |
P value = 0.358 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 1 | 30 |
subtype1 | 1 | 0 | 3 |
subtype2 | 1 | 0 | 4 |
subtype3 | 0 | 0 | 5 |
subtype4 | 0 | 0 | 9 |
subtype5 | 1 | 1 | 4 |
subtype6 | 0 | 0 | 5 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 9 | 6 | 10 | 11 |
P value = 0.65 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 36 | 18 | 0.3 - 65.0 (18.1) |
subtype1 | 9 | 2 | 0.7 - 48.8 (18.1) |
subtype2 | 6 | 5 | 0.8 - 65.0 (17.8) |
subtype3 | 10 | 5 | 1.6 - 40.1 (18.8) |
subtype4 | 11 | 6 | 0.3 - 63.8 (18.2) |
P value = 0.433 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 63.0 (12.9) |
subtype1 | 9 | 67.6 (10.7) |
subtype2 | 6 | 58.8 (11.8) |
subtype3 | 10 | 65.3 (10.3) |
subtype4 | 11 | 59.5 (16.6) |
P value = 0.5 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|
ALL | 19 | 9 | 1 | 2 | 2 | 3 |
subtype1 | 5 | 2 | 1 | 0 | 0 | 1 |
subtype2 | 2 | 2 | 0 | 2 | 0 | 0 |
subtype3 | 5 | 2 | 0 | 0 | 1 | 2 |
subtype4 | 7 | 3 | 0 | 0 | 1 | 0 |
P value = 0.681 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 19 | 12 | 5 |
subtype1 | 5 | 2 | 2 |
subtype2 | 2 | 3 | 1 |
subtype3 | 5 | 3 | 2 |
subtype4 | 7 | 4 | 0 |
P value = 0.594 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 26 | 5 |
subtype1 | 7 | 1 |
subtype2 | 4 | 0 |
subtype3 | 7 | 3 |
subtype4 | 8 | 1 |
P value = 0.229 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 28 | 5 |
subtype1 | 6 | 1 |
subtype2 | 4 | 2 |
subtype3 | 8 | 2 |
subtype4 | 10 | 0 |
P value = 0.937 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 20 | 16 |
subtype1 | 5 | 4 |
subtype2 | 3 | 3 |
subtype3 | 5 | 5 |
subtype4 | 7 | 4 |
P value = 0.712 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 2 | 31 |
subtype1 | 2 | 0 | 7 |
subtype2 | 0 | 0 | 6 |
subtype3 | 0 | 1 | 9 |
subtype4 | 1 | 1 | 9 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 8 | 10 | 4 | 5 | 5 | 4 |
P value = 0.984 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 36 | 18 | 0.3 - 65.0 (18.1) |
subtype1 | 8 | 3 | 10.2 - 48.8 (13.9) |
subtype2 | 10 | 4 | 1.6 - 40.1 (22.0) |
subtype3 | 4 | 3 | 5.6 - 63.8 (25.2) |
subtype4 | 5 | 4 | 0.7 - 65.0 (21.0) |
subtype5 | 5 | 3 | 5.1 - 31.7 (18.2) |
subtype6 | 4 | 1 | 0.3 - 35.2 (7.1) |
P value = 0.986 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 63.0 (12.9) |
subtype1 | 8 | 62.0 (11.8) |
subtype2 | 10 | 66.1 (11.3) |
subtype3 | 4 | 60.2 (19.7) |
subtype4 | 5 | 64.4 (11.8) |
subtype5 | 5 | 58.4 (18.7) |
subtype6 | 4 | 64.0 (9.8) |
P value = 0.705 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|
ALL | 19 | 9 | 1 | 2 | 2 | 3 |
subtype1 | 4 | 2 | 1 | 0 | 0 | 1 |
subtype2 | 6 | 2 | 0 | 0 | 0 | 2 |
subtype3 | 1 | 2 | 0 | 0 | 1 | 0 |
subtype4 | 2 | 2 | 0 | 1 | 0 | 0 |
subtype5 | 3 | 1 | 0 | 0 | 1 | 0 |
subtype6 | 3 | 0 | 0 | 1 | 0 | 0 |
P value = 0.905 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 19 | 12 | 5 |
subtype1 | 4 | 2 | 2 |
subtype2 | 6 | 3 | 1 |
subtype3 | 1 | 3 | 0 |
subtype4 | 2 | 2 | 1 |
subtype5 | 3 | 1 | 1 |
subtype6 | 3 | 1 | 0 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 26 | 5 |
subtype1 | 5 | 1 |
subtype2 | 8 | 2 |
subtype3 | 3 | 1 |
subtype4 | 4 | 0 |
subtype5 | 3 | 1 |
subtype6 | 3 | 0 |
P value = 0.87 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 28 | 5 |
subtype1 | 5 | 1 |
subtype2 | 8 | 2 |
subtype3 | 4 | 0 |
subtype4 | 3 | 1 |
subtype5 | 5 | 0 |
subtype6 | 3 | 1 |
P value = 0.0504 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 20 | 16 |
subtype1 | 5 | 3 |
subtype2 | 4 | 6 |
subtype3 | 3 | 1 |
subtype4 | 3 | 2 |
subtype5 | 5 | 0 |
subtype6 | 0 | 4 |
P value = 0.467 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 2 | 31 |
subtype1 | 2 | 0 | 6 |
subtype2 | 0 | 1 | 9 |
subtype3 | 1 | 0 | 3 |
subtype4 | 0 | 0 | 5 |
subtype5 | 0 | 1 | 4 |
subtype6 | 0 | 0 | 4 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 15 | 21 |
P value = 0.518 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 36 | 18 | 0.3 - 65.0 (18.1) |
subtype1 | 15 | 8 | 0.3 - 63.8 (13.4) |
subtype2 | 21 | 10 | 0.7 - 65.0 (20.6) |
P value = 0.607 (Wilcoxon-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 63.0 (12.9) |
subtype1 | 15 | 60.5 (14.8) |
subtype2 | 21 | 64.8 (11.4) |
P value = 0.98 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|
ALL | 19 | 9 | 1 | 2 | 2 | 3 |
subtype1 | 9 | 3 | 0 | 1 | 1 | 1 |
subtype2 | 10 | 6 | 1 | 1 | 1 | 2 |
P value = 0.585 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 19 | 12 | 5 |
subtype1 | 9 | 5 | 1 |
subtype2 | 10 | 7 | 4 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 26 | 5 |
subtype1 | 10 | 2 |
subtype2 | 16 | 3 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 28 | 5 |
subtype1 | 12 | 2 |
subtype2 | 16 | 3 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 20 | 16 |
subtype1 | 8 | 7 |
subtype2 | 12 | 9 |
P value = 0.777 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 2 | 31 |
subtype1 | 2 | 1 | 12 |
subtype2 | 1 | 1 | 19 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
---|---|---|---|---|---|---|---|
Number of samples | 6 | 3 | 3 | 9 | 5 | 5 | 5 |
P value = 0.675 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 36 | 18 | 0.3 - 65.0 (18.1) |
subtype1 | 6 | 2 | 5.1 - 18.1 (13.9) |
subtype2 | 3 | 2 | 8.9 - 24.4 (23.3) |
subtype3 | 3 | 0 | 10.2 - 48.8 (20.9) |
subtype4 | 9 | 6 | 0.3 - 63.8 (13.4) |
subtype5 | 5 | 2 | 1.6 - 35.5 (12.7) |
subtype6 | 5 | 3 | 0.7 - 65.0 (21.0) |
subtype7 | 5 | 3 | 23.1 - 46.1 (33.4) |
P value = 0.174 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 63.0 (12.9) |
subtype1 | 6 | 51.3 (16.8) |
subtype2 | 3 | 65.7 (7.1) |
subtype3 | 3 | 69.0 (8.5) |
subtype4 | 9 | 62.6 (14.9) |
subtype5 | 5 | 72.8 (7.9) |
subtype6 | 5 | 66.2 (9.8) |
subtype7 | 5 | 59.6 (7.1) |
P value = 0.967 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|
ALL | 19 | 9 | 1 | 2 | 2 | 3 |
subtype1 | 3 | 2 | 0 | 0 | 0 | 1 |
subtype2 | 2 | 0 | 0 | 0 | 0 | 1 |
subtype3 | 1 | 1 | 1 | 0 | 0 | 0 |
subtype4 | 5 | 2 | 0 | 1 | 1 | 0 |
subtype5 | 3 | 1 | 0 | 0 | 1 | 0 |
subtype6 | 3 | 2 | 0 | 0 | 0 | 0 |
subtype7 | 2 | 1 | 0 | 1 | 0 | 1 |
P value = 0.909 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 19 | 12 | 5 |
subtype1 | 3 | 2 | 1 |
subtype2 | 2 | 1 | 0 |
subtype3 | 1 | 1 | 1 |
subtype4 | 5 | 4 | 0 |
subtype5 | 3 | 1 | 1 |
subtype6 | 3 | 2 | 0 |
subtype7 | 2 | 1 | 2 |
P value = 0.983 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 26 | 5 |
subtype1 | 4 | 1 |
subtype2 | 2 | 1 |
subtype3 | 3 | 0 |
subtype4 | 6 | 1 |
subtype5 | 4 | 1 |
subtype6 | 4 | 0 |
subtype7 | 3 | 1 |
P value = 0.563 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 28 | 5 |
subtype1 | 4 | 1 |
subtype2 | 2 | 1 |
subtype3 | 3 | 0 |
subtype4 | 7 | 1 |
subtype5 | 5 | 0 |
subtype6 | 4 | 0 |
subtype7 | 3 | 2 |
P value = 0.556 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 20 | 16 |
subtype1 | 5 | 1 |
subtype2 | 1 | 2 |
subtype3 | 2 | 1 |
subtype4 | 4 | 5 |
subtype5 | 2 | 3 |
subtype6 | 2 | 3 |
subtype7 | 4 | 1 |
P value = 0.714 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 2 | 31 |
subtype1 | 1 | 1 | 4 |
subtype2 | 0 | 0 | 3 |
subtype3 | 1 | 0 | 2 |
subtype4 | 1 | 0 | 8 |
subtype5 | 0 | 0 | 5 |
subtype6 | 0 | 0 | 5 |
subtype7 | 0 | 1 | 4 |
-
Cluster data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CHOL-TP/15087707/CHOL-TP.mergedcluster.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CHOL-TP/15076818/CHOL-TP.merged_data.txt
-
Number of patients = 36
-
Number of clustering approaches = 10
-
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 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.