(primary solid tumor 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 11 clinical features across 134 patients, 3 significant findings detected with P value < 0.05 and Q value < 0.25.
-
6 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes correlate to 'LYMPH.NODE.METASTASIS' and 'NUMBER.OF.LYMPH.NODES'.
-
4 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 4 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 3 subtypes that do not correlate to any clinical features.
-
Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'LYMPH.NODE.METASTASIS'.
-
3 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 |
Statistical Tests |
Copy Number Ratio CNMF subtypes |
METHLYATION CNMF |
RPPA CNMF subtypes |
RPPA cHierClus subtypes |
RNAseq CNMF subtypes |
RNAseq cHierClus subtypes |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
Time to Death | logrank test |
0.0524 (1.00) |
0.57 (1.00) |
0.245 (1.00) |
0.485 (1.00) |
0.675 (1.00) |
0.95 (1.00) |
0.578 (1.00) |
0.155 (1.00) |
AGE | ANOVA |
0.0705 (1.00) |
0.0565 (1.00) |
0.473 (1.00) |
0.227 (1.00) |
0.713 (1.00) |
0.776 (1.00) |
0.134 (1.00) |
0.231 (1.00) |
GENDER | Fisher's exact test |
0.551 (1.00) |
0.055 (1.00) |
0.633 (1.00) |
0.166 (1.00) |
0.236 (1.00) |
0.178 (1.00) |
0.0768 (1.00) |
0.0203 (1.00) |
KARNOFSKY PERFORMANCE SCORE | ANOVA |
0.698 (1.00) |
0.854 (1.00) |
0.465 (1.00) |
0.359 (1.00) |
0.877 (1.00) |
0.962 (1.00) |
0.735 (1.00) |
0.152 (1.00) |
NUMBERPACKYEARSSMOKED | ANOVA |
0.549 (1.00) |
0.996 (1.00) |
0.657 (1.00) |
0.943 (1.00) |
0.737 (1.00) |
0.552 (1.00) |
0.518 (1.00) |
0.274 (1.00) |
TOBACCOSMOKINGHISTORYINDICATOR | ANOVA |
0.543 (1.00) |
0.52 (1.00) |
0.258 (1.00) |
0.512 (1.00) |
0.606 (1.00) |
0.278 (1.00) |
0.925 (1.00) |
0.0698 (1.00) |
DISTANT METASTASIS | Chi-square test |
0.467 (1.00) |
0.728 (1.00) |
0.108 (1.00) |
0.142 (1.00) |
0.404 (1.00) |
0.239 (1.00) |
0.65 (1.00) |
0.852 (1.00) |
LYMPH NODE METASTASIS | Chi-square test |
0.00261 (0.204) |
0.0539 (1.00) |
0.082 (1.00) |
0.556 (1.00) |
0.13 (1.00) |
0.000813 (0.065) |
0.0132 (1.00) |
0.325 (1.00) |
NUMBER OF LYMPH NODES | ANOVA |
0.00141 (0.111) |
0.2 (1.00) |
0.201 (1.00) |
0.697 (1.00) |
0.975 (1.00) |
0.116 (1.00) |
0.291 (1.00) |
0.309 (1.00) |
TUMOR STAGECODE | ANOVA | ||||||||
NEOPLASM DISEASESTAGE | Chi-square test |
0.0803 (1.00) |
0.0883 (1.00) |
0.279 (1.00) |
0.512 (1.00) |
0.674 (1.00) |
0.303 (1.00) |
0.0519 (1.00) |
0.151 (1.00) |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 14 | 43 | 21 | 27 | 11 | 15 |
P value = 0.0524 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 124 | 32 | 0.1 - 131.2 (7.0) |
subtype1 | 14 | 2 | 2.2 - 118.9 (7.5) |
subtype2 | 41 | 12 | 0.1 - 131.2 (7.0) |
subtype3 | 20 | 5 | 0.4 - 100.5 (6.6) |
subtype4 | 24 | 5 | 0.5 - 46.8 (8.5) |
subtype5 | 11 | 5 | 3.6 - 12.9 (6.9) |
subtype6 | 14 | 3 | 1.0 - 75.3 (4.3) |
P value = 0.0705 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 130 | 67.4 (10.6) |
subtype1 | 14 | 67.6 (11.3) |
subtype2 | 43 | 67.4 (10.8) |
subtype3 | 21 | 67.4 (9.0) |
subtype4 | 26 | 63.7 (12.0) |
subtype5 | 11 | 65.6 (7.3) |
subtype6 | 15 | 74.4 (8.6) |
P value = 0.551 (Chi-square test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 33 | 98 |
subtype1 | 1 | 13 |
subtype2 | 12 | 31 |
subtype3 | 5 | 16 |
subtype4 | 6 | 21 |
subtype5 | 4 | 7 |
subtype6 | 5 | 10 |
P value = 0.698 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 37 | 78.1 (16.3) |
subtype1 | 5 | 86.0 (5.5) |
subtype2 | 8 | 75.0 (20.7) |
subtype3 | 7 | 78.6 (18.6) |
subtype4 | 11 | 78.2 (16.6) |
subtype5 | 2 | 85.0 (7.1) |
subtype6 | 4 | 70.0 (16.3) |
P value = 0.549 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 81 | 36.6 (23.0) |
subtype1 | 12 | 33.1 (35.8) |
subtype2 | 22 | 32.0 (17.8) |
subtype3 | 15 | 35.9 (20.3) |
subtype4 | 14 | 39.0 (15.2) |
subtype5 | 8 | 50.0 (22.6) |
subtype6 | 10 | 38.1 (27.8) |
P value = 0.543 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 125 | 2.6 (1.1) |
subtype1 | 13 | 2.9 (1.0) |
subtype2 | 40 | 2.4 (1.1) |
subtype3 | 20 | 2.6 (1.2) |
subtype4 | 27 | 2.8 (1.3) |
subtype5 | 10 | 2.8 (1.1) |
subtype6 | 15 | 2.4 (1.1) |
P value = 0.467 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 75 | 4 | 51 |
subtype1 | 7 | 1 | 6 |
subtype2 | 23 | 1 | 19 |
subtype3 | 9 | 0 | 11 |
subtype4 | 20 | 0 | 7 |
subtype5 | 7 | 1 | 3 |
subtype6 | 9 | 1 | 5 |
P value = 0.00261 (Chi-square test), Q value = 0.2
nPatients | N0 | N1 | N2 | N3 | NX |
---|---|---|---|---|---|
ALL | 74 | 14 | 26 | 4 | 10 |
subtype1 | 4 | 2 | 2 | 1 | 5 |
subtype2 | 32 | 3 | 6 | 1 | 1 |
subtype3 | 10 | 1 | 6 | 0 | 3 |
subtype4 | 18 | 2 | 5 | 0 | 0 |
subtype5 | 5 | 3 | 1 | 1 | 1 |
subtype6 | 5 | 3 | 6 | 1 | 0 |
P value = 0.00141 (ANOVA), Q value = 0.11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 98 | 1.9 (3.8) |
subtype1 | 10 | 1.6 (2.6) |
subtype2 | 34 | 0.9 (1.8) |
subtype3 | 15 | 1.1 (1.3) |
subtype4 | 17 | 1.5 (2.3) |
subtype5 | 8 | 2.0 (4.1) |
subtype6 | 14 | 5.8 (7.4) |
P value = 0.0803 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 1 | 36 | 43 | 46 |
subtype1 | 1 | 4 | 3 | 6 |
subtype2 | 0 | 11 | 21 | 10 |
subtype3 | 0 | 8 | 4 | 8 |
subtype4 | 0 | 7 | 10 | 7 |
subtype5 | 0 | 3 | 3 | 5 |
subtype6 | 0 | 3 | 2 | 10 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 34 | 46 | 33 | 21 |
P value = 0.57 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 127 | 33 | 0.1 - 131.2 (6.9) |
subtype1 | 33 | 6 | 0.8 - 118.9 (6.7) |
subtype2 | 45 | 15 | 0.4 - 131.2 (7.8) |
subtype3 | 28 | 5 | 0.7 - 37.8 (6.4) |
subtype4 | 21 | 7 | 0.1 - 46.8 (7.2) |
P value = 0.0565 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 133 | 67.4 (10.5) |
subtype1 | 33 | 67.8 (10.1) |
subtype2 | 46 | 68.6 (9.6) |
subtype3 | 33 | 63.3 (12.2) |
subtype4 | 21 | 70.5 (9.3) |
P value = 0.055 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 34 | 100 |
subtype1 | 10 | 24 |
subtype2 | 16 | 30 |
subtype3 | 3 | 30 |
subtype4 | 5 | 16 |
P value = 0.854 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 38 | 78.4 (16.2) |
subtype1 | 7 | 82.9 (15.0) |
subtype2 | 10 | 79.0 (15.2) |
subtype3 | 16 | 76.2 (18.9) |
subtype4 | 5 | 78.0 (13.0) |
P value = 0.996 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 82 | 37.1 (23.2) |
subtype1 | 22 | 36.7 (28.1) |
subtype2 | 32 | 36.8 (21.2) |
subtype3 | 21 | 38.2 (21.7) |
subtype4 | 7 | 36.7 (24.9) |
P value = 0.52 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 128 | 2.6 (1.1) |
subtype1 | 32 | 2.4 (1.1) |
subtype2 | 43 | 2.6 (1.0) |
subtype3 | 33 | 2.8 (1.3) |
subtype4 | 20 | 2.5 (1.1) |
P value = 0.728 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 78 | 4 | 51 |
subtype1 | 19 | 2 | 12 |
subtype2 | 25 | 1 | 20 |
subtype3 | 20 | 0 | 13 |
subtype4 | 14 | 1 | 6 |
P value = 0.0539 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 | N3 | NX |
---|---|---|---|---|---|
ALL | 76 | 14 | 27 | 4 | 10 |
subtype1 | 12 | 5 | 11 | 1 | 4 |
subtype2 | 32 | 5 | 5 | 2 | 2 |
subtype3 | 24 | 3 | 3 | 1 | 2 |
subtype4 | 8 | 1 | 8 | 0 | 2 |
P value = 0.2 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 98 | 1.9 (3.8) |
subtype1 | 24 | 2.2 (3.5) |
subtype2 | 36 | 1.1 (2.4) |
subtype3 | 24 | 1.7 (4.7) |
subtype4 | 14 | 3.6 (4.8) |
P value = 0.0883 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 1 | 37 | 44 | 47 |
subtype1 | 1 | 7 | 8 | 17 |
subtype2 | 0 | 11 | 21 | 12 |
subtype3 | 0 | 13 | 11 | 8 |
subtype4 | 0 | 6 | 4 | 10 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 12 | 10 | 14 | 17 |
P value = 0.245 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 52 | 20 | 0.4 - 118.9 (8.3) |
subtype1 | 12 | 4 | 5.7 - 49.9 (10.9) |
subtype2 | 10 | 5 | 1.8 - 100.5 (5.5) |
subtype3 | 13 | 2 | 0.5 - 19.5 (6.6) |
subtype4 | 17 | 9 | 0.4 - 118.9 (14.9) |
P value = 0.473 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 52 | 67.3 (9.8) |
subtype1 | 12 | 63.9 (9.2) |
subtype2 | 10 | 69.5 (9.3) |
subtype3 | 13 | 66.5 (10.2) |
subtype4 | 17 | 69.1 (10.3) |
P value = 0.633 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 21 | 32 |
subtype1 | 6 | 6 |
subtype2 | 5 | 5 |
subtype3 | 5 | 9 |
subtype4 | 5 | 12 |
P value = 0.465 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 80.0 (16.7) |
subtype1 | 5 | 88.0 (4.5) |
subtype2 | 1 | 70.0 (NA) |
subtype3 | 1 | 60.0 (NA) |
subtype4 | 4 | 77.5 (25.0) |
P value = 0.657 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 27 | 32.1 (17.5) |
subtype1 | 9 | 27.6 (12.4) |
subtype2 | 5 | 28.8 (18.4) |
subtype3 | 6 | 35.2 (20.4) |
subtype4 | 7 | 37.9 (21.6) |
P value = 0.258 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 48 | 2.3 (1.1) |
subtype1 | 12 | 2.6 (0.9) |
subtype2 | 8 | 1.9 (0.8) |
subtype3 | 14 | 2.1 (1.1) |
subtype4 | 14 | 2.6 (1.2) |
P value = 0.108 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 41 | 2 | 10 |
subtype1 | 7 | 2 | 3 |
subtype2 | 10 | 0 | 0 |
subtype3 | 11 | 0 | 3 |
subtype4 | 13 | 0 | 4 |
P value = 0.082 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 | N3 | NX |
---|---|---|---|---|---|
ALL | 33 | 5 | 11 | 1 | 2 |
subtype1 | 9 | 1 | 0 | 0 | 2 |
subtype2 | 4 | 1 | 5 | 0 | 0 |
subtype3 | 10 | 0 | 3 | 0 | 0 |
subtype4 | 10 | 3 | 3 | 1 | 0 |
P value = 0.201 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 34 | 1.5 (3.0) |
subtype1 | 5 | 0.0 (0.0) |
subtype2 | 7 | 3.4 (4.1) |
subtype3 | 9 | 0.9 (1.5) |
subtype4 | 13 | 1.5 (3.3) |
P value = 0.279 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 1 | 11 | 19 | 18 |
subtype1 | 1 | 5 | 4 | 2 |
subtype2 | 0 | 2 | 2 | 6 |
subtype3 | 0 | 2 | 6 | 3 |
subtype4 | 0 | 2 | 7 | 7 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 14 | 15 | 24 |
P value = 0.485 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 52 | 20 | 0.4 - 118.9 (8.3) |
subtype1 | 14 | 9 | 0.4 - 118.9 (10.4) |
subtype2 | 15 | 5 | 1.9 - 49.9 (8.3) |
subtype3 | 23 | 6 | 0.5 - 100.5 (6.6) |
P value = 0.227 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 52 | 67.3 (9.8) |
subtype1 | 14 | 70.5 (9.0) |
subtype2 | 15 | 64.2 (9.6) |
subtype3 | 23 | 67.4 (10.2) |
P value = 0.166 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 21 | 32 |
subtype1 | 5 | 9 |
subtype2 | 9 | 6 |
subtype3 | 7 | 17 |
P value = 0.359 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 80.0 (16.7) |
subtype1 | 3 | 73.3 (28.9) |
subtype2 | 4 | 90.0 (0.0) |
subtype3 | 4 | 75.0 (12.9) |
P value = 0.943 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 27 | 32.1 (17.5) |
subtype1 | 5 | 33.0 (23.3) |
subtype2 | 9 | 30.4 (15.6) |
subtype3 | 13 | 33.0 (17.8) |
P value = 0.512 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 48 | 2.3 (1.1) |
subtype1 | 11 | 2.6 (1.2) |
subtype2 | 14 | 2.4 (0.9) |
subtype3 | 23 | 2.2 (1.1) |
P value = 0.142 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 41 | 2 | 10 |
subtype1 | 10 | 0 | 4 |
subtype2 | 10 | 2 | 3 |
subtype3 | 21 | 0 | 3 |
P value = 0.556 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 | N3 | NX |
---|---|---|---|---|---|
ALL | 33 | 5 | 11 | 1 | 2 |
subtype1 | 8 | 2 | 3 | 1 | 0 |
subtype2 | 11 | 1 | 1 | 0 | 1 |
subtype3 | 14 | 2 | 7 | 0 | 1 |
P value = 0.697 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 34 | 1.5 (3.0) |
subtype1 | 10 | 1.9 (3.7) |
subtype2 | 8 | 0.8 (1.5) |
subtype3 | 16 | 1.7 (3.1) |
P value = 0.512 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 1 | 11 | 19 | 18 |
subtype1 | 0 | 2 | 5 | 6 |
subtype2 | 0 | 6 | 5 | 4 |
subtype3 | 1 | 3 | 9 | 8 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 49 | 33 | 35 |
P value = 0.675 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 110 | 31 | 0.1 - 131.2 (7.1) |
subtype1 | 44 | 9 | 0.1 - 100.5 (6.5) |
subtype2 | 32 | 12 | 1.3 - 131.2 (6.7) |
subtype3 | 34 | 10 | 0.4 - 75.3 (8.1) |
P value = 0.713 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 116 | 66.9 (10.8) |
subtype1 | 48 | 65.9 (11.7) |
subtype2 | 33 | 67.9 (9.1) |
subtype3 | 35 | 67.2 (11.3) |
P value = 0.236 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 32 | 85 |
subtype1 | 10 | 39 |
subtype2 | 9 | 24 |
subtype3 | 13 | 22 |
P value = 0.877 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 34 | 77.6 (16.9) |
subtype1 | 19 | 78.4 (16.8) |
subtype2 | 5 | 74.0 (11.4) |
subtype3 | 10 | 78.0 (20.4) |
P value = 0.737 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 69 | 35.4 (22.5) |
subtype1 | 24 | 38.1 (28.2) |
subtype2 | 22 | 32.8 (18.1) |
subtype3 | 23 | 35.1 (20.1) |
P value = 0.606 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 111 | 2.6 (1.1) |
subtype1 | 46 | 2.5 (1.3) |
subtype2 | 32 | 2.7 (1.0) |
subtype3 | 33 | 2.7 (1.0) |
P value = 0.404 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 70 | 3 | 43 |
subtype1 | 32 | 1 | 15 |
subtype2 | 17 | 2 | 14 |
subtype3 | 21 | 0 | 14 |
P value = 0.13 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 | N3 | NX |
---|---|---|---|---|---|
ALL | 68 | 11 | 23 | 4 | 9 |
subtype1 | 25 | 4 | 13 | 0 | 6 |
subtype2 | 20 | 2 | 8 | 2 | 1 |
subtype3 | 23 | 5 | 2 | 2 | 2 |
P value = 0.975 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 88 | 1.9 (3.9) |
subtype1 | 31 | 2.0 (3.1) |
subtype2 | 31 | 1.9 (3.9) |
subtype3 | 26 | 1.8 (4.8) |
P value = 0.674 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 1 | 34 | 38 | 40 |
subtype1 | 1 | 15 | 13 | 17 |
subtype2 | 0 | 7 | 14 | 12 |
subtype3 | 0 | 12 | 11 | 11 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 37 | 18 | 62 |
P value = 0.95 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 110 | 31 | 0.1 - 131.2 (7.1) |
subtype1 | 36 | 9 | 0.4 - 75.3 (7.9) |
subtype2 | 17 | 7 | 4.5 - 131.2 (7.3) |
subtype3 | 57 | 15 | 0.1 - 100.5 (6.4) |
P value = 0.776 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 116 | 66.9 (10.8) |
subtype1 | 37 | 67.6 (11.2) |
subtype2 | 18 | 65.4 (9.2) |
subtype3 | 61 | 66.9 (11.1) |
P value = 0.178 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 32 | 85 |
subtype1 | 14 | 23 |
subtype2 | 5 | 13 |
subtype3 | 13 | 49 |
P value = 0.962 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 34 | 77.6 (16.9) |
subtype1 | 10 | 78.0 (20.4) |
subtype2 | 3 | 80.0 (10.0) |
subtype3 | 21 | 77.1 (16.5) |
P value = 0.552 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 69 | 35.4 (22.5) |
subtype1 | 24 | 31.7 (17.5) |
subtype2 | 13 | 35.0 (20.7) |
subtype3 | 32 | 38.4 (26.4) |
P value = 0.278 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 111 | 2.6 (1.1) |
subtype1 | 36 | 2.7 (1.1) |
subtype2 | 16 | 2.9 (0.9) |
subtype3 | 59 | 2.5 (1.2) |
P value = 0.239 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 70 | 3 | 43 |
subtype1 | 21 | 0 | 16 |
subtype2 | 9 | 0 | 9 |
subtype3 | 40 | 3 | 18 |
P value = 0.000813 (Chi-square test), Q value = 0.065
nPatients | N0 | N1 | N2 | N3 | NX |
---|---|---|---|---|---|
ALL | 68 | 11 | 23 | 4 | 9 |
subtype1 | 25 | 6 | 1 | 2 | 2 |
subtype2 | 14 | 0 | 1 | 2 | 1 |
subtype3 | 29 | 5 | 21 | 0 | 6 |
P value = 0.116 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 88 | 1.9 (3.9) |
subtype1 | 29 | 1.6 (4.5) |
subtype2 | 16 | 0.4 (1.0) |
subtype3 | 43 | 2.7 (4.0) |
P value = 0.303 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 1 | 34 | 38 | 40 |
subtype1 | 0 | 11 | 14 | 11 |
subtype2 | 0 | 6 | 9 | 3 |
subtype3 | 1 | 17 | 15 | 26 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 32 | 54 | 45 |
P value = 0.578 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 124 | 31 | 0.1 - 131.2 (7.0) |
subtype1 | 28 | 4 | 0.8 - 118.9 (5.4) |
subtype2 | 51 | 12 | 0.4 - 49.9 (7.0) |
subtype3 | 45 | 15 | 0.1 - 131.2 (8.2) |
P value = 0.134 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 130 | 67.3 (10.6) |
subtype1 | 31 | 69.7 (11.3) |
subtype2 | 54 | 65.2 (10.8) |
subtype3 | 45 | 68.2 (9.6) |
P value = 0.0768 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 33 | 98 |
subtype1 | 4 | 28 |
subtype2 | 13 | 41 |
subtype3 | 16 | 29 |
P value = 0.735 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 38 | 78.4 (16.2) |
subtype1 | 7 | 82.9 (9.5) |
subtype2 | 24 | 77.5 (18.9) |
subtype3 | 7 | 77.1 (11.1) |
P value = 0.518 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 36.7 (23.1) |
subtype1 | 20 | 35.0 (27.9) |
subtype2 | 36 | 34.6 (18.1) |
subtype3 | 24 | 41.2 (25.7) |
P value = 0.925 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 125 | 2.6 (1.1) |
subtype1 | 31 | 2.6 (1.3) |
subtype2 | 54 | 2.6 (1.1) |
subtype3 | 40 | 2.7 (1.1) |
P value = 0.65 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 76 | 3 | 51 |
subtype1 | 17 | 1 | 13 |
subtype2 | 33 | 0 | 21 |
subtype3 | 26 | 2 | 17 |
P value = 0.0132 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 | N3 | NX |
---|---|---|---|---|---|
ALL | 75 | 13 | 26 | 4 | 10 |
subtype1 | 15 | 6 | 6 | 2 | 2 |
subtype2 | 36 | 5 | 4 | 2 | 6 |
subtype3 | 24 | 2 | 16 | 0 | 2 |
P value = 0.291 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 98 | 1.9 (3.8) |
subtype1 | 25 | 2.4 (5.0) |
subtype2 | 37 | 1.1 (2.6) |
subtype3 | 36 | 2.3 (3.8) |
P value = 0.0519 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 1 | 37 | 43 | 45 |
subtype1 | 1 | 6 | 8 | 15 |
subtype2 | 0 | 20 | 21 | 11 |
subtype3 | 0 | 11 | 14 | 19 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 7 | 29 | 95 |
P value = 0.155 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 124 | 31 | 0.1 - 131.2 (7.0) |
subtype1 | 7 | 2 | 1.4 - 7.8 (5.5) |
subtype2 | 25 | 4 | 0.8 - 118.9 (5.2) |
subtype3 | 92 | 25 | 0.1 - 131.2 (7.7) |
P value = 0.231 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 130 | 67.3 (10.6) |
subtype1 | 7 | 72.3 (8.3) |
subtype2 | 28 | 69.0 (11.6) |
subtype3 | 95 | 66.4 (10.4) |
P value = 0.0203 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 33 | 98 |
subtype1 | 0 | 7 |
subtype2 | 3 | 26 |
subtype3 | 30 | 65 |
P value = 0.152 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 38 | 78.4 (16.2) |
subtype1 | 1 | 80.0 (NA) |
subtype2 | 8 | 83.8 (9.2) |
subtype3 | 29 | 76.9 (17.7) |
P value = 0.274 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 36.7 (23.1) |
subtype1 | 6 | 23.3 (20.5) |
subtype2 | 18 | 40.9 (29.4) |
subtype3 | 56 | 36.7 (20.9) |
P value = 0.0698 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 125 | 2.6 (1.1) |
subtype1 | 7 | 3.6 (0.8) |
subtype2 | 28 | 2.5 (1.3) |
subtype3 | 90 | 2.6 (1.1) |
P value = 0.852 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 76 | 3 | 51 |
subtype1 | 4 | 0 | 3 |
subtype2 | 14 | 1 | 13 |
subtype3 | 58 | 2 | 35 |
P value = 0.325 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 | N3 | NX |
---|---|---|---|---|---|
ALL | 75 | 13 | 26 | 4 | 10 |
subtype1 | 5 | 1 | 1 | 0 | 0 |
subtype2 | 12 | 6 | 6 | 2 | 2 |
subtype3 | 58 | 6 | 19 | 2 | 8 |
P value = 0.309 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 98 | 1.9 (3.8) |
subtype1 | 7 | 0.7 (1.5) |
subtype2 | 22 | 2.9 (5.3) |
subtype3 | 69 | 1.7 (3.3) |
P value = 0.151 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 1 | 37 | 43 | 45 |
subtype1 | 0 | 1 | 3 | 3 |
subtype2 | 1 | 5 | 7 | 14 |
subtype3 | 0 | 31 | 33 | 28 |
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Cluster data file = BLCA-TP.mergedcluster.txt
-
Clinical data file = BLCA-TP.clin.merged.picked.txt
-
Number of patients = 134
-
Number of clustering approaches = 8
-
Number of selected clinical features = 11
-
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, one-way analysis of variance (Howell 2002) was applied to compare the clinical values between tumor subtypes using 'anova' 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 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.