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 39 patients, 2 significant findings detected with P value < 0.05 and Q value < 0.25.
-
4 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes do not correlate to any clinical features.
-
4 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 4 subtypes that correlate to 'Time to Death'.
-
Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 4 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.
-
5 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes do not correlate to any clinical features.
-
3 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes do not correlate to any clinical features.
-
6 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes correlate to 'Time to Death'.
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
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 |
Copy Number Ratio CNMF subtypes |
0.295 (1.00) |
0.655 (1.00) |
0.144 (1.00) |
0.066 (1.00) |
0.587 (1.00) |
0.834 (1.00) |
0.0523 (1.00) |
METHLYATION CNMF |
0.857 (1.00) |
0.0333 (1.00) |
0.261 (1.00) |
0.254 (1.00) |
0.781 (1.00) |
1 (1.00) |
0.779 (1.00) |
RNAseq CNMF subtypes |
0.00226 (0.124) |
0.473 (1.00) |
0.847 (1.00) |
0.669 (1.00) |
0.4 (1.00) |
0.682 (1.00) |
0.21 (1.00) |
RNAseq cHierClus subtypes |
0.00926 (0.5) |
0.0582 (1.00) |
0.31 (1.00) |
0.441 (1.00) |
0.982 (1.00) |
0.0996 (1.00) |
0.0626 (1.00) |
MIRSEQ CNMF |
0.207 (1.00) |
0.502 (1.00) |
0.932 (1.00) |
0.677 (1.00) |
0.46 (1.00) |
0.752 (1.00) |
0.679 (1.00) |
MIRSEQ CHIERARCHICAL |
0.248 (1.00) |
0.478 (1.00) |
0.562 (1.00) |
0.654 (1.00) |
0.495 (1.00) |
0.85 (1.00) |
0.894 (1.00) |
MIRseq Mature CNMF subtypes |
0.81 (1.00) |
0.41 (1.00) |
0.487 (1.00) |
0.932 (1.00) |
0.0332 (1.00) |
0.548 (1.00) |
0.483 (1.00) |
MIRseq Mature cHierClus subtypes |
0.00032 (0.0179) |
0.511 (1.00) |
0.188 (1.00) |
0.168 (1.00) |
0.346 (1.00) |
0.155 (1.00) |
0.897 (1.00) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 7 | 12 | 14 | 6 |
P value = 0.295 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 39 | 29 | 0.2 - 91.7 (13.3) |
subtype1 | 7 | 6 | 2.8 - 91.7 (31.2) |
subtype2 | 12 | 8 | 1.9 - 23.9 (12.8) |
subtype3 | 14 | 12 | 0.2 - 29.0 (17.6) |
subtype4 | 6 | 3 | 1.6 - 51.8 (7.0) |
P value = 0.655 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 39 | 64.8 (8.4) |
subtype1 | 7 | 65.0 (9.6) |
subtype2 | 12 | 64.4 (8.6) |
subtype3 | 14 | 63.1 (7.0) |
subtype4 | 6 | 69.2 (10.1) |
P value = 0.144 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 3 | 1 | 1 | 11 | 19 | 4 |
subtype1 | 1 | 0 | 0 | 4 | 1 | 1 |
subtype2 | 1 | 0 | 0 | 4 | 7 | 0 |
subtype3 | 0 | 0 | 1 | 2 | 8 | 3 |
subtype4 | 1 | 1 | 0 | 1 | 3 | 0 |
P value = 0.066 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 7 | 17 | 15 |
subtype1 | 2 | 5 | 0 |
subtype2 | 1 | 5 | 6 |
subtype3 | 1 | 6 | 7 |
subtype4 | 3 | 1 | 2 |
P value = 0.587 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 25 | 6 | 5 |
subtype1 | 6 | 1 | 0 |
subtype2 | 9 | 1 | 2 |
subtype3 | 6 | 2 | 3 |
subtype4 | 4 | 2 | 0 |
P value = 0.834 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 31 | 2 | 6 |
subtype1 | 5 | 1 | 1 |
subtype2 | 11 | 0 | 1 |
subtype3 | 10 | 1 | 3 |
subtype4 | 5 | 0 | 1 |
P value = 0.0523 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 10 | 29 |
subtype1 | 0 | 7 |
subtype2 | 3 | 9 |
subtype3 | 3 | 11 |
subtype4 | 4 | 2 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 7 | 6 | 12 | 14 |
P value = 0.857 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 39 | 29 | 0.2 - 91.7 (13.3) |
subtype1 | 7 | 6 | 1.9 - 91.7 (15.0) |
subtype2 | 6 | 4 | 0.2 - 23.6 (10.3) |
subtype3 | 12 | 9 | 2.5 - 29.0 (13.9) |
subtype4 | 14 | 10 | 1.6 - 80.8 (8.5) |
P value = 0.0333 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 39 | 64.8 (8.4) |
subtype1 | 7 | 55.4 (7.3) |
subtype2 | 6 | 67.2 (2.2) |
subtype3 | 12 | 66.8 (7.8) |
subtype4 | 14 | 66.8 (8.3) |
P value = 0.261 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 3 | 1 | 1 | 11 | 19 | 4 |
subtype1 | 0 | 0 | 0 | 5 | 1 | 1 |
subtype2 | 0 | 0 | 1 | 1 | 4 | 0 |
subtype3 | 1 | 0 | 0 | 3 | 6 | 2 |
subtype4 | 2 | 1 | 0 | 2 | 8 | 1 |
P value = 0.254 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 7 | 17 | 15 |
subtype1 | 0 | 5 | 2 |
subtype2 | 1 | 2 | 3 |
subtype3 | 1 | 7 | 4 |
subtype4 | 5 | 3 | 6 |
P value = 0.781 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 25 | 6 | 5 |
subtype1 | 6 | 0 | 1 |
subtype2 | 4 | 0 | 1 |
subtype3 | 7 | 3 | 1 |
subtype4 | 8 | 3 | 2 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 31 | 2 | 6 |
subtype1 | 6 | 0 | 1 |
subtype2 | 5 | 0 | 1 |
subtype3 | 9 | 1 | 2 |
subtype4 | 11 | 1 | 2 |
P value = 0.779 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 10 | 29 |
subtype1 | 1 | 6 |
subtype2 | 2 | 4 |
subtype3 | 4 | 8 |
subtype4 | 3 | 11 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 13 | 7 | 10 | 9 |
P value = 0.00226 (logrank test), Q value = 0.12
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 39 | 29 | 0.2 - 91.7 (13.3) |
subtype1 | 13 | 9 | 8.0 - 91.7 (17.9) |
subtype2 | 7 | 4 | 3.5 - 51.8 (18.8) |
subtype3 | 10 | 10 | 0.2 - 31.2 (4.9) |
subtype4 | 9 | 6 | 1.6 - 29.0 (6.6) |
P value = 0.473 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 39 | 64.8 (8.4) |
subtype1 | 13 | 64.2 (7.4) |
subtype2 | 7 | 61.6 (5.7) |
subtype3 | 10 | 65.8 (10.1) |
subtype4 | 9 | 67.1 (9.8) |
P value = 0.847 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 3 | 1 | 1 | 11 | 19 | 4 |
subtype1 | 2 | 0 | 0 | 5 | 4 | 2 |
subtype2 | 0 | 0 | 0 | 2 | 5 | 0 |
subtype3 | 0 | 1 | 1 | 2 | 5 | 1 |
subtype4 | 1 | 0 | 0 | 2 | 5 | 1 |
P value = 0.669 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 7 | 17 | 15 |
subtype1 | 2 | 8 | 3 |
subtype2 | 1 | 3 | 3 |
subtype3 | 3 | 3 | 4 |
subtype4 | 1 | 3 | 5 |
P value = 0.4 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 25 | 6 | 5 |
subtype1 | 9 | 1 | 3 |
subtype2 | 3 | 3 | 1 |
subtype3 | 7 | 1 | 0 |
subtype4 | 6 | 1 | 1 |
P value = 0.682 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 31 | 2 | 6 |
subtype1 | 9 | 1 | 3 |
subtype2 | 6 | 0 | 1 |
subtype3 | 7 | 1 | 2 |
subtype4 | 9 | 0 | 0 |
P value = 0.21 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 10 | 29 |
subtype1 | 2 | 11 |
subtype2 | 3 | 4 |
subtype3 | 1 | 9 |
subtype4 | 4 | 5 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 9 | 14 | 8 | 8 |
P value = 0.00926 (logrank test), Q value = 0.5
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 39 | 29 | 0.2 - 91.7 (13.3) |
subtype1 | 9 | 6 | 8.0 - 91.7 (23.8) |
subtype2 | 14 | 10 | 1.9 - 51.8 (13.8) |
subtype3 | 8 | 8 | 0.2 - 31.2 (4.9) |
subtype4 | 8 | 5 | 1.6 - 29.0 (7.3) |
P value = 0.0582 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 39 | 64.8 (8.4) |
subtype1 | 9 | 62.2 (8.0) |
subtype2 | 14 | 61.0 (8.4) |
subtype3 | 8 | 69.4 (7.2) |
subtype4 | 8 | 69.8 (6.2) |
P value = 0.31 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 3 | 1 | 1 | 11 | 19 | 4 |
subtype1 | 1 | 0 | 0 | 4 | 2 | 2 |
subtype2 | 1 | 0 | 0 | 5 | 8 | 0 |
subtype3 | 0 | 1 | 1 | 1 | 4 | 1 |
subtype4 | 1 | 0 | 0 | 1 | 5 | 1 |
P value = 0.441 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 7 | 17 | 15 |
subtype1 | 1 | 6 | 2 |
subtype2 | 2 | 7 | 5 |
subtype3 | 3 | 2 | 3 |
subtype4 | 1 | 2 | 5 |
P value = 0.982 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 25 | 6 | 5 |
subtype1 | 6 | 1 | 2 |
subtype2 | 9 | 3 | 2 |
subtype3 | 5 | 1 | 0 |
subtype4 | 5 | 1 | 1 |
P value = 0.0996 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 31 | 2 | 6 |
subtype1 | 5 | 1 | 3 |
subtype2 | 13 | 0 | 1 |
subtype3 | 5 | 1 | 2 |
subtype4 | 8 | 0 | 0 |
P value = 0.0626 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 10 | 29 |
subtype1 | 1 | 8 |
subtype2 | 5 | 9 |
subtype3 | 0 | 8 |
subtype4 | 4 | 4 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 13 | 11 | 8 |
P value = 0.207 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 32 | 23 | 0.2 - 51.8 (12.8) |
subtype1 | 13 | 11 | 0.2 - 29.0 (5.2) |
subtype2 | 11 | 6 | 3.5 - 51.8 (17.3) |
subtype3 | 8 | 6 | 1.9 - 31.2 (9.7) |
P value = 0.502 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 32 | 64.5 (8.0) |
subtype1 | 13 | 65.2 (7.6) |
subtype2 | 11 | 63.1 (7.6) |
subtype3 | 8 | 65.4 (9.8) |
P value = 0.932 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|---|
ALL | 2 | 1 | 8 | 17 | 4 |
subtype1 | 1 | 1 | 3 | 6 | 2 |
subtype2 | 1 | 0 | 2 | 6 | 2 |
subtype3 | 0 | 0 | 3 | 5 | 0 |
P value = 0.677 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 5 | 13 | 14 |
subtype1 | 3 | 4 | 6 |
subtype2 | 2 | 5 | 4 |
subtype3 | 0 | 4 | 4 |
P value = 0.46 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 19 | 5 | 5 |
subtype1 | 7 | 1 | 2 |
subtype2 | 5 | 3 | 3 |
subtype3 | 7 | 1 | 0 |
P value = 0.752 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 26 | 2 | 4 |
subtype1 | 10 | 1 | 2 |
subtype2 | 8 | 1 | 2 |
subtype3 | 8 | 0 | 0 |
P value = 0.679 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 8 | 24 |
subtype1 | 3 | 10 |
subtype2 | 2 | 9 |
subtype3 | 3 | 5 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 3 | 11 | 8 | 4 | 6 |
P value = 0.248 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 32 | 23 | 0.2 - 51.8 (12.8) |
subtype1 | 3 | 3 | 3.5 - 23.6 (15.0) |
subtype2 | 11 | 6 | 2.5 - 51.8 (13.6) |
subtype3 | 8 | 5 | 1.6 - 21.4 (7.8) |
subtype4 | 4 | 4 | 0.2 - 23.9 (5.0) |
subtype5 | 6 | 5 | 6.5 - 29.0 (16.2) |
P value = 0.478 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 32 | 64.5 (8.0) |
subtype1 | 3 | 65.0 (2.0) |
subtype2 | 11 | 63.4 (7.6) |
subtype3 | 8 | 63.4 (9.2) |
subtype4 | 4 | 71.2 (6.8) |
subtype5 | 6 | 63.5 (9.5) |
P value = 0.562 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|---|
ALL | 2 | 1 | 8 | 17 | 4 |
subtype1 | 0 | 0 | 1 | 2 | 0 |
subtype2 | 0 | 0 | 3 | 7 | 1 |
subtype3 | 0 | 0 | 3 | 4 | 1 |
subtype4 | 1 | 1 | 0 | 2 | 0 |
subtype5 | 1 | 0 | 1 | 2 | 2 |
P value = 0.654 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 5 | 13 | 14 |
subtype1 | 0 | 2 | 1 |
subtype2 | 1 | 6 | 4 |
subtype3 | 1 | 3 | 4 |
subtype4 | 2 | 0 | 2 |
subtype5 | 1 | 2 | 3 |
P value = 0.495 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 19 | 5 | 5 |
subtype1 | 2 | 0 | 1 |
subtype2 | 5 | 4 | 2 |
subtype3 | 6 | 1 | 0 |
subtype4 | 2 | 0 | 1 |
subtype5 | 4 | 0 | 1 |
P value = 0.85 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 26 | 2 | 4 |
subtype1 | 3 | 0 | 0 |
subtype2 | 9 | 0 | 2 |
subtype3 | 6 | 1 | 1 |
subtype4 | 3 | 0 | 1 |
subtype5 | 5 | 1 | 0 |
P value = 0.894 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 8 | 24 |
subtype1 | 0 | 3 |
subtype2 | 3 | 8 |
subtype3 | 3 | 5 |
subtype4 | 1 | 3 |
subtype5 | 1 | 5 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 12 | 8 | 10 |
P value = 0.81 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 30 | 21 | 0.2 - 51.8 (13.5) |
subtype1 | 12 | 7 | 1.9 - 51.8 (12.8) |
subtype2 | 8 | 7 | 0.2 - 29.0 (16.2) |
subtype3 | 10 | 7 | 1.6 - 31.2 (14.4) |
P value = 0.41 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 30 | 64.6 (8.2) |
subtype1 | 12 | 61.1 (9.4) |
subtype2 | 8 | 67.6 (6.2) |
subtype3 | 10 | 66.3 (7.3) |
P value = 0.487 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|---|
ALL | 2 | 1 | 8 | 15 | 4 |
subtype1 | 1 | 0 | 5 | 5 | 1 |
subtype2 | 1 | 1 | 2 | 3 | 1 |
subtype3 | 0 | 0 | 1 | 7 | 2 |
P value = 0.932 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 5 | 13 | 12 |
subtype1 | 2 | 6 | 4 |
subtype2 | 2 | 3 | 3 |
subtype3 | 1 | 4 | 5 |
P value = 0.0332 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 17 | 5 | 5 |
subtype1 | 10 | 2 | 0 |
subtype2 | 4 | 0 | 1 |
subtype3 | 3 | 3 | 4 |
P value = 0.548 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 24 | 2 | 4 |
subtype1 | 9 | 1 | 2 |
subtype2 | 6 | 0 | 2 |
subtype3 | 9 | 1 | 0 |
P value = 0.483 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 7 | 23 |
subtype1 | 4 | 8 |
subtype2 | 2 | 6 |
subtype3 | 1 | 9 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 3 | 7 | 3 | 6 | 6 | 5 |
P value = 0.00032 (logrank test), Q value = 0.018
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 30 | 21 | 0.2 - 51.8 (13.5) |
subtype1 | 3 | 2 | 13.6 - 15.1 (14.3) |
subtype2 | 7 | 4 | 2.5 - 51.8 (13.3) |
subtype3 | 3 | 1 | 10.9 - 23.8 (21.4) |
subtype4 | 6 | 4 | 1.9 - 31.2 (15.1) |
subtype5 | 6 | 5 | 0.2 - 5.2 (3.7) |
subtype6 | 5 | 5 | 6.5 - 29.0 (17.3) |
P value = 0.511 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 30 | 64.6 (8.2) |
subtype1 | 3 | 65.7 (9.7) |
subtype2 | 7 | 59.9 (8.9) |
subtype3 | 3 | 68.7 (8.3) |
subtype4 | 6 | 65.8 (7.1) |
subtype5 | 6 | 68.5 (7.1) |
subtype6 | 5 | 61.8 (8.9) |
P value = 0.188 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|---|
ALL | 2 | 1 | 8 | 15 | 4 |
subtype1 | 1 | 0 | 1 | 0 | 1 |
subtype2 | 0 | 0 | 3 | 4 | 0 |
subtype3 | 0 | 0 | 2 | 1 | 0 |
subtype4 | 0 | 0 | 0 | 5 | 1 |
subtype5 | 1 | 1 | 0 | 3 | 1 |
subtype6 | 0 | 0 | 2 | 2 | 1 |
P value = 0.168 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 5 | 13 | 12 |
subtype1 | 1 | 2 | 0 |
subtype2 | 1 | 4 | 2 |
subtype3 | 0 | 2 | 1 |
subtype4 | 0 | 2 | 4 |
subtype5 | 3 | 0 | 3 |
subtype6 | 0 | 3 | 2 |
P value = 0.346 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 17 | 5 | 5 |
subtype1 | 3 | 0 | 0 |
subtype2 | 4 | 3 | 0 |
subtype3 | 2 | 0 | 1 |
subtype4 | 2 | 1 | 3 |
subtype5 | 3 | 1 | 0 |
subtype6 | 3 | 0 | 1 |
P value = 0.155 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 24 | 2 | 4 |
subtype1 | 1 | 1 | 1 |
subtype2 | 6 | 0 | 1 |
subtype3 | 3 | 0 | 0 |
subtype4 | 6 | 0 | 0 |
subtype5 | 3 | 1 | 2 |
subtype6 | 5 | 0 | 0 |
P value = 0.897 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 7 | 23 |
subtype1 | 0 | 3 |
subtype2 | 2 | 5 |
subtype3 | 0 | 3 |
subtype4 | 2 | 4 |
subtype5 | 2 | 4 |
subtype6 | 1 | 4 |
-
Cluster data file = MESO-TP.mergedcluster.txt
-
Clinical data file = MESO-TP.merged_data.txt
-
Number of patients = 39
-
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 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.