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 82 patients, 12 significant findings detected with P value < 0.05 and Q value < 0.25.
-
5 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes correlate to 'Time to Death' and 'PATHOLOGY.N.STAGE'.
-
5 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'Time to Death' and 'GENDER'.
-
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 correlate to 'Time to Death' and 'NEOPLASM.DISEASESTAGE'.
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3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'NEOPLASM.DISEASESTAGE'.
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5 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes correlate to 'NEOPLASM.DISEASESTAGE'.
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3 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes correlate to 'NEOPLASM.DISEASESTAGE'.
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6 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes correlate to 'Time to Death' and 'NEOPLASM.DISEASESTAGE'.
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
GENDER | ETHNICITY |
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 |
0.0019 (0.0893) |
0.298 (1.00) |
0.102 (1.00) |
0.698 (1.00) |
0.00154 (0.0739) |
0.686 (1.00) |
0.683 (1.00) |
METHLYATION CNMF |
0.00134 (0.0672) |
0.337 (1.00) |
0.184 (1.00) |
0.112 (1.00) |
0.115 (1.00) |
0.00116 (0.0592) |
0.797 (1.00) |
RNAseq CNMF subtypes |
0.00144 (0.0706) |
0.938 (1.00) |
0.0262 (1.00) |
0.157 (1.00) |
0.0719 (1.00) |
0.322 (1.00) |
0.937 (1.00) |
RNAseq cHierClus subtypes |
0.00103 (0.0548) |
0.656 (1.00) |
0.00503 (0.226) |
0.0357 (1.00) |
0.0609 (1.00) |
0.473 (1.00) |
0.281 (1.00) |
MIRSEQ CNMF |
0.0147 (0.617) |
0.186 (1.00) |
0.00054 (0.0302) |
0.00595 (0.262) |
0.0399 (1.00) |
0.123 (1.00) |
0.3 (1.00) |
MIRSEQ CHIERARCHICAL |
0.0839 (1.00) |
0.275 (1.00) |
0.00074 (0.04) |
0.0913 (1.00) |
0.361 (1.00) |
0.323 (1.00) |
0.661 (1.00) |
MIRseq Mature CNMF subtypes |
0.00879 (0.378) |
0.256 (1.00) |
0.00109 (0.0567) |
0.0329 (1.00) |
0.0616 (1.00) |
0.125 (1.00) |
0.499 (1.00) |
MIRseq Mature cHierClus subtypes |
0.00219 (0.101) |
0.373 (1.00) |
0.00064 (0.0352) |
0.0349 (1.00) |
0.355 (1.00) |
0.952 (1.00) |
0.452 (1.00) |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 27 | 21 | 14 | 9 | 9 |
P value = 0.0019 (logrank test), Q value = 0.089
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 79 | 27 | 4.1 - 153.6 (31.2) |
subtype1 | 26 | 14 | 4.9 - 128.1 (33.3) |
subtype2 | 21 | 1 | 6.9 - 153.6 (31.2) |
subtype3 | 14 | 7 | 10.2 - 64.1 (20.8) |
subtype4 | 9 | 4 | 4.1 - 63.2 (27.3) |
subtype5 | 9 | 1 | 12.0 - 91.5 (46.8) |
P value = 0.298 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 46.9 (16.3) |
subtype1 | 27 | 47.1 (18.2) |
subtype2 | 21 | 51.0 (15.1) |
subtype3 | 14 | 41.1 (16.6) |
subtype4 | 9 | 51.9 (11.7) |
subtype5 | 9 | 40.2 (14.8) |
P value = 0.102 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 8 | 34 | 17 | 17 |
subtype1 | 4 | 8 | 7 | 7 |
subtype2 | 2 | 12 | 6 | 1 |
subtype3 | 0 | 4 | 3 | 7 |
subtype4 | 1 | 4 | 0 | 1 |
subtype5 | 1 | 6 | 1 | 1 |
P value = 0.698 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 8 | 39 | 11 | 18 |
subtype1 | 4 | 9 | 5 | 8 |
subtype2 | 2 | 13 | 3 | 3 |
subtype3 | 0 | 7 | 2 | 5 |
subtype4 | 1 | 4 | 0 | 1 |
subtype5 | 1 | 6 | 1 | 1 |
P value = 0.00154 (Fisher's exact test), Q value = 0.074
nPatients | 0 | 1 |
---|---|---|
ALL | 67 | 10 |
subtype1 | 24 | 2 |
subtype2 | 20 | 1 |
subtype3 | 7 | 7 |
subtype4 | 7 | 0 |
subtype5 | 9 | 0 |
P value = 0.686 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 52 | 28 |
subtype1 | 19 | 8 |
subtype2 | 13 | 8 |
subtype3 | 10 | 4 |
subtype4 | 4 | 5 |
subtype5 | 6 | 3 |
P value = 0.683 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 27 |
subtype1 | 3 | 11 |
subtype2 | 1 | 7 |
subtype3 | 4 | 6 |
subtype4 | 0 | 1 |
subtype5 | 0 | 2 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 18 | 11 | 21 | 17 | 11 |
P value = 0.00134 (logrank test), Q value = 0.067
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 78 | 26 | 4.1 - 153.6 (32.0) |
subtype1 | 18 | 12 | 4.1 - 120.3 (20.1) |
subtype2 | 11 | 3 | 12.0 - 128.1 (50.1) |
subtype3 | 21 | 7 | 6.8 - 153.6 (31.2) |
subtype4 | 17 | 3 | 6.9 - 121.2 (23.8) |
subtype5 | 11 | 1 | 12.6 - 91.5 (22.2) |
P value = 0.337 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 46.4 (16.1) |
subtype1 | 18 | 40.3 (20.0) |
subtype2 | 11 | 53.2 (14.8) |
subtype3 | 21 | 47.2 (14.5) |
subtype4 | 17 | 49.3 (12.7) |
subtype5 | 11 | 43.9 (16.4) |
P value = 0.184 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 8 | 33 | 16 | 16 |
subtype1 | 1 | 7 | 6 | 4 |
subtype2 | 1 | 3 | 4 | 3 |
subtype3 | 1 | 7 | 3 | 6 |
subtype4 | 3 | 7 | 3 | 3 |
subtype5 | 2 | 9 | 0 | 0 |
P value = 0.112 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 8 | 38 | 9 | 18 |
subtype1 | 1 | 9 | 3 | 5 |
subtype2 | 1 | 5 | 4 | 1 |
subtype3 | 1 | 8 | 1 | 7 |
subtype4 | 3 | 7 | 1 | 5 |
subtype5 | 2 | 9 | 0 | 0 |
P value = 0.115 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 64 | 10 |
subtype1 | 14 | 4 |
subtype2 | 9 | 2 |
subtype3 | 14 | 4 |
subtype4 | 16 | 0 |
subtype5 | 11 | 0 |
P value = 0.00116 (Fisher's exact test), Q value = 0.059
nPatients | FEMALE | MALE |
---|---|---|
ALL | 49 | 29 |
subtype1 | 13 | 5 |
subtype2 | 9 | 2 |
subtype3 | 7 | 14 |
subtype4 | 9 | 8 |
subtype5 | 11 | 0 |
P value = 0.797 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 28 |
subtype1 | 3 | 6 |
subtype2 | 2 | 6 |
subtype3 | 1 | 7 |
subtype4 | 2 | 5 |
subtype5 | 0 | 4 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 24 | 14 | 17 | 22 |
P value = 0.00144 (logrank test), Q value = 0.071
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 77 | 25 | 4.1 - 153.6 (32.7) |
subtype1 | 24 | 14 | 4.1 - 128.1 (20.4) |
subtype2 | 14 | 5 | 6.8 - 153.6 (33.8) |
subtype3 | 17 | 5 | 12.0 - 106.5 (50.1) |
subtype4 | 22 | 1 | 6.9 - 121.2 (28.4) |
P value = 0.938 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 77 | 46.7 (15.9) |
subtype1 | 24 | 46.7 (18.2) |
subtype2 | 14 | 47.3 (14.9) |
subtype3 | 17 | 45.0 (13.1) |
subtype4 | 22 | 47.8 (16.8) |
P value = 0.0262 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 8 | 33 | 16 | 15 |
subtype1 | 3 | 8 | 8 | 5 |
subtype2 | 0 | 6 | 2 | 6 |
subtype3 | 1 | 5 | 5 | 3 |
subtype4 | 4 | 14 | 1 | 1 |
P value = 0.157 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 8 | 38 | 8 | 18 |
subtype1 | 3 | 10 | 4 | 7 |
subtype2 | 0 | 8 | 2 | 4 |
subtype3 | 1 | 6 | 1 | 6 |
subtype4 | 4 | 14 | 1 | 1 |
P value = 0.0719 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 64 | 9 |
subtype1 | 21 | 3 |
subtype2 | 10 | 4 |
subtype3 | 12 | 2 |
subtype4 | 21 | 0 |
P value = 0.322 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 48 | 29 |
subtype1 | 16 | 8 |
subtype2 | 11 | 3 |
subtype3 | 8 | 9 |
subtype4 | 13 | 9 |
P value = 0.937 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 7 | 28 |
subtype1 | 2 | 11 |
subtype2 | 2 | 7 |
subtype3 | 2 | 5 |
subtype4 | 1 | 5 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 23 | 23 | 7 | 24 |
P value = 0.00103 (logrank test), Q value = 0.055
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 77 | 25 | 4.1 - 153.6 (32.7) |
subtype1 | 23 | 14 | 4.1 - 128.1 (33.8) |
subtype2 | 23 | 7 | 6.8 - 153.6 (39.6) |
subtype3 | 7 | 3 | 10.1 - 87.9 (19.0) |
subtype4 | 24 | 1 | 6.9 - 121.2 (27.5) |
P value = 0.656 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 77 | 46.7 (15.9) |
subtype1 | 23 | 47.3 (19.2) |
subtype2 | 23 | 45.4 (15.0) |
subtype3 | 7 | 41.3 (14.9) |
subtype4 | 24 | 49.1 (14.1) |
P value = 0.00503 (Fisher's exact test), Q value = 0.23
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 8 | 33 | 16 | 15 |
subtype1 | 2 | 9 | 7 | 5 |
subtype2 | 0 | 8 | 5 | 8 |
subtype3 | 2 | 1 | 1 | 2 |
subtype4 | 4 | 15 | 3 | 0 |
P value = 0.0357 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 8 | 38 | 8 | 18 |
subtype1 | 2 | 12 | 4 | 5 |
subtype2 | 0 | 10 | 2 | 9 |
subtype3 | 2 | 1 | 1 | 2 |
subtype4 | 4 | 15 | 1 | 2 |
P value = 0.0609 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 64 | 9 |
subtype1 | 19 | 4 |
subtype2 | 16 | 5 |
subtype3 | 6 | 0 |
subtype4 | 23 | 0 |
P value = 0.473 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 48 | 29 |
subtype1 | 17 | 6 |
subtype2 | 13 | 10 |
subtype3 | 5 | 2 |
subtype4 | 13 | 11 |
P value = 0.281 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 7 | 28 |
subtype1 | 2 | 10 |
subtype2 | 3 | 8 |
subtype3 | 2 | 3 |
subtype4 | 0 | 7 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 38 | 15 | 25 |
P value = 0.0147 (logrank test), Q value = 0.62
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 78 | 26 | 4.1 - 153.6 (32.0) |
subtype1 | 38 | 15 | 4.1 - 120.3 (29.7) |
subtype2 | 15 | 8 | 8.3 - 153.6 (33.8) |
subtype3 | 25 | 3 | 6.9 - 121.2 (46.8) |
P value = 0.186 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 46.4 (16.1) |
subtype1 | 38 | 43.0 (15.8) |
subtype2 | 15 | 50.9 (17.4) |
subtype3 | 25 | 49.0 (15.1) |
P value = 0.00054 (Fisher's exact test), Q value = 0.03
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 8 | 33 | 16 | 16 |
subtype1 | 3 | 12 | 12 | 9 |
subtype2 | 1 | 4 | 2 | 7 |
subtype3 | 4 | 17 | 2 | 0 |
P value = 0.00595 (Fisher's exact test), Q value = 0.26
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 8 | 38 | 9 | 18 |
subtype1 | 3 | 16 | 4 | 13 |
subtype2 | 1 | 5 | 3 | 5 |
subtype3 | 4 | 17 | 2 | 0 |
P value = 0.0399 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 64 | 10 |
subtype1 | 29 | 7 |
subtype2 | 11 | 3 |
subtype3 | 24 | 0 |
P value = 0.123 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 49 | 29 |
subtype1 | 25 | 13 |
subtype2 | 12 | 3 |
subtype3 | 12 | 13 |
P value = 0.3 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 28 |
subtype1 | 5 | 18 |
subtype2 | 3 | 5 |
subtype3 | 0 | 5 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 17 | 25 | 12 | 20 | 4 |
P value = 0.0839 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 78 | 26 | 4.1 - 153.6 (32.0) |
subtype1 | 17 | 7 | 4.1 - 93.4 (41.3) |
subtype2 | 25 | 7 | 6.9 - 153.6 (33.8) |
subtype3 | 12 | 0 | 10.1 - 106.5 (28.4) |
subtype4 | 20 | 10 | 4.9 - 128.1 (25.4) |
subtype5 | 4 | 2 | 23.3 - 53.0 (38.4) |
P value = 0.275 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 46.4 (16.1) |
subtype1 | 17 | 46.3 (14.3) |
subtype2 | 25 | 47.9 (15.2) |
subtype3 | 12 | 40.5 (15.9) |
subtype4 | 20 | 45.4 (18.8) |
subtype5 | 4 | 60.8 (9.8) |
P value = 0.00074 (Fisher's exact test), Q value = 0.04
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 8 | 33 | 16 | 16 |
subtype1 | 0 | 5 | 7 | 4 |
subtype2 | 1 | 17 | 0 | 6 |
subtype3 | 4 | 3 | 2 | 1 |
subtype4 | 3 | 6 | 7 | 3 |
subtype5 | 0 | 2 | 0 | 2 |
P value = 0.0913 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 8 | 38 | 9 | 18 |
subtype1 | 0 | 6 | 4 | 6 |
subtype2 | 1 | 17 | 1 | 5 |
subtype3 | 4 | 3 | 1 | 2 |
subtype4 | 3 | 9 | 3 | 4 |
subtype5 | 0 | 3 | 0 | 1 |
P value = 0.361 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 64 | 10 |
subtype1 | 13 | 3 |
subtype2 | 23 | 2 |
subtype3 | 10 | 0 |
subtype4 | 15 | 4 |
subtype5 | 3 | 1 |
P value = 0.323 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 49 | 29 |
subtype1 | 7 | 10 |
subtype2 | 16 | 9 |
subtype3 | 9 | 3 |
subtype4 | 14 | 6 |
subtype5 | 3 | 1 |
P value = 0.661 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 28 |
subtype1 | 3 | 4 |
subtype2 | 2 | 6 |
subtype3 | 1 | 6 |
subtype4 | 2 | 9 |
subtype5 | 0 | 3 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 39 | 17 | 22 |
P value = 0.00879 (logrank test), Q value = 0.38
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 78 | 26 | 4.1 - 153.6 (32.0) |
subtype1 | 39 | 15 | 4.1 - 120.3 (29.0) |
subtype2 | 17 | 10 | 12.6 - 153.6 (38.9) |
subtype3 | 22 | 1 | 6.9 - 121.2 (30.2) |
P value = 0.256 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 46.4 (16.1) |
subtype1 | 39 | 43.4 (15.8) |
subtype2 | 17 | 50.7 (17.6) |
subtype3 | 22 | 48.5 (14.8) |
P value = 0.00109 (Fisher's exact test), Q value = 0.057
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 8 | 33 | 16 | 16 |
subtype1 | 3 | 12 | 13 | 9 |
subtype2 | 1 | 7 | 1 | 7 |
subtype3 | 4 | 14 | 2 | 0 |
P value = 0.0329 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 8 | 38 | 9 | 18 |
subtype1 | 3 | 16 | 5 | 13 |
subtype2 | 1 | 8 | 2 | 5 |
subtype3 | 4 | 14 | 2 | 0 |
P value = 0.0616 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 64 | 10 |
subtype1 | 30 | 7 |
subtype2 | 13 | 3 |
subtype3 | 21 | 0 |
P value = 0.125 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 49 | 29 |
subtype1 | 26 | 13 |
subtype2 | 13 | 4 |
subtype3 | 10 | 12 |
P value = 0.499 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 28 |
subtype1 | 5 | 18 |
subtype2 | 3 | 6 |
subtype3 | 0 | 4 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 9 | 23 | 9 | 18 | 9 | 10 |
P value = 0.00219 (logrank test), Q value = 0.1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 78 | 26 | 4.1 - 153.6 (32.0) |
subtype1 | 9 | 6 | 4.1 - 64.1 (30.3) |
subtype2 | 23 | 5 | 6.9 - 153.6 (38.9) |
subtype3 | 9 | 0 | 17.4 - 106.5 (46.5) |
subtype4 | 18 | 9 | 4.9 - 120.3 (20.4) |
subtype5 | 9 | 5 | 12.6 - 128.1 (37.1) |
subtype6 | 10 | 1 | 10.1 - 93.4 (30.2) |
P value = 0.373 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 46.4 (16.1) |
subtype1 | 9 | 44.4 (15.4) |
subtype2 | 23 | 47.9 (15.8) |
subtype3 | 9 | 41.8 (12.0) |
subtype4 | 18 | 44.5 (19.4) |
subtype5 | 9 | 56.9 (10.0) |
subtype6 | 10 | 43.2 (17.5) |
P value = 0.00064 (Fisher's exact test), Q value = 0.035
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 8 | 33 | 16 | 16 |
subtype1 | 0 | 3 | 4 | 2 |
subtype2 | 1 | 17 | 0 | 4 |
subtype3 | 1 | 2 | 3 | 2 |
subtype4 | 1 | 6 | 7 | 3 |
subtype5 | 2 | 2 | 0 | 5 |
subtype6 | 3 | 3 | 2 | 0 |
P value = 0.0349 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 8 | 38 | 9 | 18 |
subtype1 | 0 | 4 | 2 | 3 |
subtype2 | 1 | 17 | 1 | 3 |
subtype3 | 1 | 2 | 1 | 4 |
subtype4 | 1 | 9 | 3 | 4 |
subtype5 | 2 | 3 | 0 | 4 |
subtype6 | 3 | 3 | 2 | 0 |
P value = 0.355 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 64 | 10 |
subtype1 | 7 | 2 |
subtype2 | 21 | 2 |
subtype3 | 8 | 0 |
subtype4 | 13 | 4 |
subtype5 | 7 | 2 |
subtype6 | 8 | 0 |
P value = 0.952 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 49 | 29 |
subtype1 | 6 | 3 |
subtype2 | 15 | 8 |
subtype3 | 5 | 4 |
subtype4 | 12 | 6 |
subtype5 | 6 | 3 |
subtype6 | 5 | 5 |
P value = 0.452 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 28 |
subtype1 | 3 | 3 |
subtype2 | 2 | 5 |
subtype3 | 1 | 4 |
subtype4 | 2 | 7 |
subtype5 | 0 | 6 |
subtype6 | 0 | 3 |
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Cluster data file = ACC-TP.mergedcluster.txt
-
Clinical data file = ACC-TP.merged_data.txt
-
Number of patients = 82
-
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.