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 77 patients, 9 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 correlate to 'Time to Death'.
-
4 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'Time to Death'.
-
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 5 subtypes that correlate to 'Time to Death'.
-
3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'Time to Death'.
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5 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes correlate to 'Time to Death'.
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3 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes correlate to 'NEOPLASM_DISEASESTAGE' and 'PATHOLOGY_N_STAGE'.
-
4 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes correlate to 'Time to Death'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
KARNOFSKY PERFORMANCE SCORE |
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 | Kruskal-Wallis (anova) |
Copy Number Ratio CNMF subtypes |
0.0137 (0.184) |
0.865 (1.00) |
0.787 (1.00) |
0.53 (0.941) |
0.851 (1.00) |
0.323 (0.827) |
0.158 (0.6) |
|
METHLYATION CNMF |
0.0171 (0.184) |
0.424 (0.941) |
0.292 (0.814) |
0.646 (1.00) |
0.562 (0.972) |
1 (1.00) |
0.469 (0.941) |
|
RNAseq CNMF subtypes |
9.78e-05 (0.00313) |
0.493 (0.941) |
0.591 (0.995) |
0.905 (1.00) |
0.0663 (0.35) |
0.705 (1.00) |
0.131 (0.561) |
|
RNAseq cHierClus subtypes |
3.6e-05 (0.00231) |
0.263 (0.801) |
0.447 (0.941) |
0.518 (0.941) |
0.205 (0.728) |
0.484 (0.941) |
0.0532 (0.31) |
|
MIRSEQ CNMF |
0.0193 (0.184) |
0.245 (0.801) |
0.981 (1.00) |
0.981 (1.00) |
0.0711 (0.35) |
1 (1.00) |
0.432 (0.941) |
|
MIRSEQ CHIERARCHICAL |
0.0288 (0.205) |
0.684 (1.00) |
0.697 (1.00) |
0.985 (1.00) |
0.625 (1.00) |
0.506 (0.941) |
0.0985 (0.45) |
|
MIRseq Mature CNMF subtypes |
0.0393 (0.251) |
0.322 (0.827) |
0.022 (0.184) |
0.279 (0.813) |
0.023 (0.184) |
1 (1.00) |
0.609 (0.999) |
|
MIRseq Mature cHierClus subtypes |
0.00169 (0.0361) |
0.25 (0.801) |
0.693 (1.00) |
0.963 (1.00) |
0.339 (0.834) |
0.394 (0.935) |
0.159 (0.6) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 18 | 25 | 21 | 13 |
P value = 0.0137 (logrank test), Q value = 0.18
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 76 | 65 | 0.7 - 91.7 (15.1) |
subtype1 | 18 | 15 | 1.6 - 91.7 (28.7) |
subtype2 | 25 | 22 | 1.9 - 41.5 (14.3) |
subtype3 | 20 | 18 | 0.7 - 29.0 (16.2) |
subtype4 | 13 | 10 | 1.3 - 62.3 (8.4) |
P value = 0.865 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 77 | 63.0 (9.4) |
subtype1 | 18 | 65.1 (8.7) |
subtype2 | 25 | 62.3 (8.8) |
subtype3 | 21 | 62.9 (7.9) |
subtype4 | 13 | 61.5 (13.4) |
P value = 0.787 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 7 | 2 | 1 | 16 | 40 | 11 |
subtype1 | 1 | 1 | 0 | 6 | 8 | 2 |
subtype2 | 3 | 0 | 0 | 4 | 16 | 2 |
subtype3 | 2 | 0 | 1 | 4 | 10 | 4 |
subtype4 | 1 | 1 | 0 | 2 | 6 | 3 |
P value = 0.53 (Fisher's exact test), Q value = 0.94
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 14 | 25 | 28 | 8 |
subtype1 | 3 | 9 | 4 | 1 |
subtype2 | 4 | 6 | 12 | 2 |
subtype3 | 3 | 8 | 7 | 3 |
subtype4 | 4 | 2 | 5 | 2 |
P value = 0.851 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 42 | 10 | 21 |
subtype1 | 12 | 2 | 4 |
subtype2 | 13 | 3 | 9 |
subtype3 | 11 | 2 | 4 |
subtype4 | 6 | 3 | 4 |
P value = 0.323 (Fisher's exact test), Q value = 0.83
nPatients | 0 | 1 |
---|---|---|
ALL | 49 | 2 |
subtype1 | 8 | 1 |
subtype2 | 17 | 0 |
subtype3 | 14 | 1 |
subtype4 | 10 | 0 |
P value = 0.158 (Fisher's exact test), Q value = 0.6
nPatients | FEMALE | MALE |
---|---|---|
ALL | 15 | 62 |
subtype1 | 1 | 17 |
subtype2 | 5 | 20 |
subtype3 | 4 | 17 |
subtype4 | 5 | 8 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 13 | 17 | 23 | 24 |
P value = 0.0171 (logrank test), Q value = 0.18
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 76 | 65 | 0.7 - 91.7 (15.1) |
subtype1 | 13 | 9 | 1.9 - 91.7 (24.3) |
subtype2 | 16 | 16 | 0.7 - 41.5 (12.7) |
subtype3 | 23 | 20 | 1.3 - 32.3 (18.8) |
subtype4 | 24 | 20 | 1.6 - 80.8 (14.9) |
P value = 0.424 (Kruskal-Wallis (anova)), Q value = 0.94
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 77 | 63.0 (9.4) |
subtype1 | 13 | 59.4 (8.4) |
subtype2 | 17 | 63.6 (8.2) |
subtype3 | 23 | 62.5 (10.6) |
subtype4 | 24 | 64.9 (9.3) |
P value = 0.292 (Fisher's exact test), Q value = 0.81
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 7 | 2 | 1 | 16 | 40 | 11 |
subtype1 | 0 | 0 | 0 | 7 | 4 | 2 |
subtype2 | 2 | 0 | 1 | 3 | 9 | 2 |
subtype3 | 3 | 0 | 0 | 3 | 13 | 4 |
subtype4 | 2 | 2 | 0 | 3 | 14 | 3 |
P value = 0.646 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 14 | 25 | 28 | 8 |
subtype1 | 2 | 7 | 2 | 2 |
subtype2 | 3 | 5 | 6 | 2 |
subtype3 | 3 | 7 | 10 | 3 |
subtype4 | 6 | 6 | 10 | 1 |
P value = 0.562 (Fisher's exact test), Q value = 0.97
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 42 | 10 | 21 |
subtype1 | 10 | 0 | 3 |
subtype2 | 9 | 1 | 5 |
subtype3 | 12 | 4 | 6 |
subtype4 | 11 | 5 | 7 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 49 | 2 |
subtype1 | 9 | 0 |
subtype2 | 8 | 0 |
subtype3 | 16 | 1 |
subtype4 | 16 | 1 |
P value = 0.469 (Fisher's exact test), Q value = 0.94
nPatients | FEMALE | MALE |
---|---|---|
ALL | 15 | 62 |
subtype1 | 1 | 12 |
subtype2 | 2 | 15 |
subtype3 | 6 | 17 |
subtype4 | 6 | 18 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 23 | 19 | 16 | 19 |
P value = 9.78e-05 (logrank test), Q value = 0.0031
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 76 | 65 | 0.7 - 91.7 (15.1) |
subtype1 | 23 | 19 | 4.4 - 91.7 (23.8) |
subtype2 | 18 | 13 | 1.3 - 62.3 (18.3) |
subtype3 | 16 | 16 | 0.7 - 42.8 (4.9) |
subtype4 | 19 | 17 | 2.5 - 29.0 (14.7) |
P value = 0.493 (Kruskal-Wallis (anova)), Q value = 0.94
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 77 | 63.0 (9.4) |
subtype1 | 23 | 64.1 (7.1) |
subtype2 | 19 | 59.4 (11.8) |
subtype3 | 16 | 64.4 (9.4) |
subtype4 | 19 | 63.9 (8.7) |
P value = 0.591 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 7 | 2 | 1 | 16 | 40 | 11 |
subtype1 | 2 | 1 | 0 | 7 | 10 | 3 |
subtype2 | 0 | 0 | 0 | 3 | 13 | 3 |
subtype3 | 1 | 1 | 1 | 3 | 7 | 3 |
subtype4 | 4 | 0 | 0 | 3 | 10 | 2 |
P value = 0.905 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 14 | 25 | 28 | 8 |
subtype1 | 4 | 10 | 6 | 2 |
subtype2 | 2 | 5 | 8 | 3 |
subtype3 | 4 | 5 | 6 | 1 |
subtype4 | 4 | 5 | 8 | 2 |
P value = 0.0663 (Fisher's exact test), Q value = 0.35
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 42 | 10 | 21 |
subtype1 | 15 | 1 | 7 |
subtype2 | 5 | 5 | 8 |
subtype3 | 11 | 1 | 2 |
subtype4 | 11 | 3 | 4 |
P value = 0.705 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 49 | 2 |
subtype1 | 14 | 1 |
subtype2 | 13 | 0 |
subtype3 | 10 | 1 |
subtype4 | 12 | 0 |
P value = 0.131 (Fisher's exact test), Q value = 0.56
nPatients | FEMALE | MALE |
---|---|---|
ALL | 15 | 62 |
subtype1 | 3 | 20 |
subtype2 | 7 | 12 |
subtype3 | 1 | 15 |
subtype4 | 4 | 15 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 19 | 12 | 18 | 13 | 15 |
P value = 3.6e-05 (logrank test), Q value = 0.0023
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 76 | 65 | 0.7 - 91.7 (15.1) |
subtype1 | 19 | 14 | 4.4 - 91.7 (26.1) |
subtype2 | 12 | 12 | 1.9 - 23.6 (12.7) |
subtype3 | 17 | 13 | 1.3 - 62.3 (17.7) |
subtype4 | 13 | 13 | 0.7 - 42.8 (4.7) |
subtype5 | 15 | 13 | 2.5 - 29.0 (16.4) |
P value = 0.263 (Kruskal-Wallis (anova)), Q value = 0.8
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 77 | 63.0 (9.4) |
subtype1 | 19 | 63.9 (7.7) |
subtype2 | 12 | 61.4 (9.2) |
subtype3 | 18 | 58.6 (11.6) |
subtype4 | 13 | 66.6 (8.6) |
subtype5 | 15 | 65.3 (7.6) |
P value = 0.447 (Fisher's exact test), Q value = 0.94
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 7 | 2 | 1 | 16 | 40 | 11 |
subtype1 | 1 | 1 | 0 | 6 | 8 | 3 |
subtype2 | 2 | 0 | 0 | 4 | 6 | 0 |
subtype3 | 0 | 0 | 0 | 3 | 11 | 4 |
subtype4 | 1 | 1 | 1 | 2 | 6 | 2 |
subtype5 | 3 | 0 | 0 | 1 | 9 | 2 |
P value = 0.518 (Fisher's exact test), Q value = 0.94
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 14 | 25 | 28 | 8 |
subtype1 | 4 | 8 | 5 | 2 |
subtype2 | 2 | 6 | 3 | 0 |
subtype3 | 1 | 5 | 8 | 3 |
subtype4 | 4 | 4 | 4 | 1 |
subtype5 | 3 | 2 | 8 | 2 |
P value = 0.205 (Fisher's exact test), Q value = 0.73
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 42 | 10 | 21 |
subtype1 | 12 | 1 | 6 |
subtype2 | 8 | 1 | 3 |
subtype3 | 5 | 4 | 8 |
subtype4 | 9 | 1 | 1 |
subtype5 | 8 | 3 | 3 |
P value = 0.484 (Fisher's exact test), Q value = 0.94
nPatients | 0 | 1 |
---|---|---|
ALL | 49 | 2 |
subtype1 | 10 | 1 |
subtype2 | 10 | 0 |
subtype3 | 11 | 0 |
subtype4 | 8 | 1 |
subtype5 | 10 | 0 |
P value = 0.0532 (Fisher's exact test), Q value = 0.31
nPatients | FEMALE | MALE |
---|---|---|
ALL | 15 | 62 |
subtype1 | 2 | 17 |
subtype2 | 2 | 10 |
subtype3 | 7 | 11 |
subtype4 | 0 | 13 |
subtype5 | 4 | 11 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 32 | 27 | 18 |
P value = 0.0193 (logrank test), Q value = 0.18
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 76 | 65 | 0.7 - 91.7 (15.1) |
subtype1 | 32 | 28 | 0.7 - 56.4 (14.9) |
subtype2 | 26 | 20 | 1.3 - 91.7 (19.4) |
subtype3 | 18 | 17 | 1.9 - 42.8 (10.9) |
P value = 0.245 (Kruskal-Wallis (anova)), Q value = 0.8
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 77 | 63.0 (9.4) |
subtype1 | 32 | 63.2 (7.8) |
subtype2 | 27 | 60.8 (11.2) |
subtype3 | 18 | 65.8 (8.3) |
P value = 0.981 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 7 | 2 | 1 | 16 | 40 | 11 |
subtype1 | 4 | 1 | 1 | 7 | 15 | 4 |
subtype2 | 2 | 0 | 0 | 5 | 16 | 4 |
subtype3 | 1 | 1 | 0 | 4 | 9 | 3 |
P value = 0.981 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 14 | 25 | 28 | 8 |
subtype1 | 7 | 10 | 11 | 3 |
subtype2 | 5 | 9 | 9 | 3 |
subtype3 | 2 | 6 | 8 | 2 |
P value = 0.0711 (Fisher's exact test), Q value = 0.35
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 42 | 10 | 21 |
subtype1 | 17 | 1 | 11 |
subtype2 | 12 | 6 | 8 |
subtype3 | 13 | 3 | 2 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 49 | 2 |
subtype1 | 18 | 1 |
subtype2 | 17 | 1 |
subtype3 | 14 | 0 |
P value = 0.432 (Fisher's exact test), Q value = 0.94
nPatients | FEMALE | MALE |
---|---|---|
ALL | 15 | 62 |
subtype1 | 4 | 28 |
subtype2 | 7 | 20 |
subtype3 | 4 | 14 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 24 | 23 | 6 | 12 | 12 |
P value = 0.0288 (logrank test), Q value = 0.2
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 76 | 65 | 0.7 - 91.7 (15.1) |
subtype1 | 24 | 20 | 0.7 - 56.4 (14.3) |
subtype2 | 22 | 19 | 2.5 - 62.3 (14.9) |
subtype3 | 6 | 6 | 1.9 - 42.8 (9.7) |
subtype4 | 12 | 11 | 1.3 - 27.7 (13.7) |
subtype5 | 12 | 9 | 14.3 - 91.7 (28.1) |
P value = 0.684 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 77 | 63.0 (9.4) |
subtype1 | 24 | 63.7 (7.1) |
subtype2 | 23 | 62.5 (10.1) |
subtype3 | 6 | 67.2 (10.4) |
subtype4 | 12 | 58.8 (13.0) |
subtype5 | 12 | 64.6 (6.6) |
P value = 0.697 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 7 | 2 | 1 | 16 | 40 | 11 |
subtype1 | 4 | 0 | 1 | 5 | 10 | 4 |
subtype2 | 0 | 0 | 0 | 5 | 15 | 3 |
subtype3 | 0 | 1 | 0 | 1 | 3 | 1 |
subtype4 | 1 | 1 | 0 | 3 | 6 | 1 |
subtype5 | 2 | 0 | 0 | 2 | 6 | 2 |
P value = 0.985 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 14 | 25 | 28 | 8 |
subtype1 | 6 | 7 | 7 | 3 |
subtype2 | 3 | 9 | 7 | 3 |
subtype3 | 1 | 1 | 4 | 0 |
subtype4 | 2 | 4 | 5 | 1 |
subtype5 | 2 | 4 | 5 | 1 |
P value = 0.625 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 42 | 10 | 21 |
subtype1 | 13 | 2 | 7 |
subtype2 | 9 | 6 | 7 |
subtype3 | 5 | 0 | 1 |
subtype4 | 7 | 1 | 4 |
subtype5 | 8 | 1 | 2 |
P value = 0.506 (Fisher's exact test), Q value = 0.94
nPatients | 0 | 1 |
---|---|---|
ALL | 49 | 2 |
subtype1 | 12 | 1 |
subtype2 | 17 | 0 |
subtype3 | 5 | 0 |
subtype4 | 8 | 0 |
subtype5 | 7 | 1 |
P value = 0.0985 (Fisher's exact test), Q value = 0.45
nPatients | FEMALE | MALE |
---|---|---|
ALL | 15 | 62 |
subtype1 | 1 | 23 |
subtype2 | 7 | 16 |
subtype3 | 2 | 4 |
subtype4 | 3 | 9 |
subtype5 | 2 | 10 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 33 | 23 | 19 |
P value = 0.0393 (logrank test), Q value = 0.25
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 74 | 63 | 0.7 - 91.7 (15.3) |
subtype1 | 32 | 26 | 2.5 - 91.7 (19.4) |
subtype2 | 23 | 19 | 0.7 - 32.3 (17.3) |
subtype3 | 19 | 18 | 1.6 - 42.8 (10.9) |
P value = 0.322 (Kruskal-Wallis (anova)), Q value = 0.83
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 75 | 63.0 (9.5) |
subtype1 | 33 | 61.4 (8.9) |
subtype2 | 23 | 62.4 (10.5) |
subtype3 | 19 | 66.4 (8.7) |
P value = 0.022 (Fisher's exact test), Q value = 0.18
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 7 | 2 | 1 | 16 | 38 | 11 |
subtype1 | 2 | 0 | 0 | 12 | 15 | 4 |
subtype2 | 5 | 0 | 1 | 2 | 11 | 4 |
subtype3 | 0 | 2 | 0 | 2 | 12 | 3 |
P value = 0.279 (Fisher's exact test), Q value = 0.81
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 14 | 25 | 26 | 8 |
subtype1 | 4 | 16 | 10 | 3 |
subtype2 | 7 | 4 | 8 | 3 |
subtype3 | 3 | 5 | 8 | 2 |
P value = 0.023 (Fisher's exact test), Q value = 0.18
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 40 | 10 | 21 |
subtype1 | 23 | 5 | 4 |
subtype2 | 10 | 1 | 9 |
subtype3 | 7 | 4 | 8 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 47 | 2 |
subtype1 | 21 | 1 |
subtype2 | 13 | 1 |
subtype3 | 13 | 0 |
P value = 0.609 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 14 | 61 |
subtype1 | 8 | 25 |
subtype2 | 3 | 20 |
subtype3 | 3 | 16 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 14 | 15 | 19 | 27 |
P value = 0.00169 (logrank test), Q value = 0.036
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 74 | 63 | 0.7 - 91.7 (15.3) |
subtype1 | 14 | 11 | 11.9 - 91.7 (29.7) |
subtype2 | 14 | 12 | 2.5 - 62.3 (15.1) |
subtype3 | 19 | 15 | 1.9 - 42.8 (13.3) |
subtype4 | 27 | 25 | 0.7 - 29.0 (13.6) |
P value = 0.25 (Kruskal-Wallis (anova)), Q value = 0.8
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 75 | 63.0 (9.5) |
subtype1 | 14 | 63.4 (7.2) |
subtype2 | 15 | 59.5 (8.7) |
subtype3 | 19 | 66.2 (9.2) |
subtype4 | 27 | 62.4 (10.7) |
P value = 0.693 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 7 | 2 | 1 | 16 | 38 | 11 |
subtype1 | 2 | 0 | 0 | 5 | 5 | 2 |
subtype2 | 0 | 0 | 0 | 3 | 10 | 2 |
subtype3 | 1 | 2 | 0 | 4 | 9 | 3 |
subtype4 | 4 | 0 | 1 | 4 | 14 | 4 |
P value = 0.963 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 14 | 25 | 26 | 8 |
subtype1 | 2 | 7 | 3 | 1 |
subtype2 | 2 | 5 | 6 | 2 |
subtype3 | 4 | 5 | 7 | 2 |
subtype4 | 6 | 8 | 10 | 3 |
P value = 0.339 (Fisher's exact test), Q value = 0.83
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 40 | 10 | 21 |
subtype1 | 11 | 1 | 2 |
subtype2 | 6 | 4 | 4 |
subtype3 | 11 | 3 | 5 |
subtype4 | 12 | 2 | 10 |
P value = 0.394 (Fisher's exact test), Q value = 0.94
nPatients | 0 | 1 |
---|---|---|
ALL | 47 | 2 |
subtype1 | 6 | 1 |
subtype2 | 10 | 0 |
subtype3 | 15 | 0 |
subtype4 | 16 | 1 |
P value = 0.159 (Fisher's exact test), Q value = 0.6
nPatients | FEMALE | MALE |
---|---|---|
ALL | 14 | 61 |
subtype1 | 1 | 13 |
subtype2 | 6 | 9 |
subtype3 | 3 | 16 |
subtype4 | 4 | 23 |
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Cluster data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/MESO-TP/15104504/MESO-TP.mergedcluster.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/MESO-TP/15084766/MESO-TP.merged_data.txt
-
Number of patients = 77
-
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 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.