(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 8 clinical features across 101 patients, 8 significant findings detected with P value < 0.05 and Q value < 0.25.
-
CNMF clustering analysis on array-based mRNA expression data identified 2 subtypes that do not correlate to any clinical features.
-
Consensus hierarchical clustering analysis on array-based mRNA expression data identified 3 subtypes that do not correlate to any clinical features.
-
3 subtypes identified in current cancer cohort by 'CN CNMF'. These subtypes do not correlate to any clinical features.
-
3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'PATHOLOGY.T' and 'TUMOR.STAGE'.
-
CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'PATHOLOGY.T' and 'TUMOR.STAGE'.
-
Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'GENDER', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
-
CNMF clustering analysis on sequencing-based miR expression data identified 3 subtypes that do not correlate to any clinical features.
-
Consensus hierarchical clustering analysis on sequencing-based miR expression data identified 3 subtypes that do not correlate to any clinical features.
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
Statistical Tests | logrank test | ANOVA | Fisher's exact test | ANOVA | Chi-square test | Chi-square test | Chi-square test | Chi-square test |
mRNA CNMF subtypes |
100 (1.00) |
0.182 (1.00) |
0.585 (1.00) |
0.0623 (1.00) |
1 (1.00) |
0.292 (1.00) |
||
mRNA cHierClus subtypes |
100 (1.00) |
0.948 (1.00) |
1 (1.00) |
0.216 (1.00) |
1 (1.00) |
|||
CN CNMF |
0.156 (1.00) |
0.875 (1.00) |
0.488 (1.00) |
0.311 (1.00) |
0.415 (1.00) |
0.451 (1.00) |
0.51 (1.00) |
0.297 (1.00) |
METHLYATION CNMF |
0.15 (1.00) |
0.0523 (1.00) |
0.226 (1.00) |
0.144 (1.00) |
6.37e-08 (3.69e-06) |
0.142 (1.00) |
0.0567 (1.00) |
7.93e-06 (0.000452) |
RNAseq CNMF subtypes |
0.0277 (1.00) |
0.00648 (0.324) |
0.0242 (1.00) |
0.000102 (0.00552) |
0.636 (1.00) |
0.0115 (0.564) |
9.52e-05 (0.00524) |
|
RNAseq cHierClus subtypes |
0.0127 (0.607) |
0.454 (1.00) |
0.000595 (0.031) |
0.578 (1.00) |
0.000293 (0.0155) |
0.0583 (1.00) |
0.00397 (0.202) |
2.81e-05 (0.00157) |
MIRseq CNMF subtypes |
0.582 (1.00) |
0.574 (1.00) |
0.178 (1.00) |
0.295 (1.00) |
0.137 (1.00) |
0.267 (1.00) |
0.266 (1.00) |
0.0296 (1.00) |
MIRseq cHierClus subtypes |
0.693 (1.00) |
0.925 (1.00) |
0.0974 (1.00) |
0.647 (1.00) |
0.0183 (0.858) |
0.262 (1.00) |
0.239 (1.00) |
0.0732 (1.00) |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 7 | 9 |
P value = 100 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 16 | 2 | 0.5 - 58.5 (7.8) |
subtype1 | 7 | 1 | 0.5 - 53.8 (5.9) |
subtype2 | 9 | 1 | 1.1 - 58.5 (10.8) |
P value = 0.182 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 16 | 57.9 (11.5) |
subtype1 | 7 | 53.6 (10.3) |
subtype2 | 9 | 61.3 (11.7) |
P value = 0.585 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 4 | 12 |
subtype1 | 1 | 6 |
subtype2 | 3 | 6 |
P value = 0.0623 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 7 | 7 | 2 |
subtype1 | 1 | 4 | 2 |
subtype2 | 6 | 3 | 0 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 |
---|---|---|
ALL | 9 | 1 |
subtype1 | 4 | 1 |
subtype2 | 5 | 0 |
P value = 0.292 (Chi-square test), Q value = 1
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 5 | 2 | 1 | 1 |
subtype1 | 1 | 1 | 1 | 1 |
subtype2 | 4 | 1 | 0 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 4 | 7 | 5 |
P value = 100 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 16 | 2 | 0.5 - 58.5 (7.8) |
subtype1 | 4 | 1 | 10.8 - 58.5 (40.4) |
subtype2 | 7 | 1 | 0.5 - 25.1 (4.4) |
subtype3 | 5 | 0 | 0.7 - 53.8 (4.1) |
P value = 0.948 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 16 | 57.9 (11.5) |
subtype1 | 4 | 57.0 (5.0) |
subtype2 | 7 | 57.4 (13.0) |
subtype3 | 5 | 59.4 (14.8) |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 4 | 12 |
subtype1 | 1 | 3 |
subtype2 | 2 | 5 |
subtype3 | 1 | 4 |
P value = 0.216 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 7 | 7 | 2 |
subtype1 | 3 | 1 | 0 |
subtype2 | 1 | 4 | 2 |
subtype3 | 3 | 2 | 0 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 |
---|---|---|
ALL | 9 | 1 |
subtype1 | 2 | 0 |
subtype2 | 4 | 1 |
subtype3 | 3 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 27 | 54 | 20 |
P value = 0.156 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 94 | 14 | 0.0 - 182.7 (13.9) |
subtype1 | 24 | 3 | 0.0 - 182.7 (10.4) |
subtype2 | 50 | 7 | 0.2 - 129.9 (23.7) |
subtype3 | 20 | 4 | 0.1 - 79.8 (11.1) |
P value = 0.875 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 98 | 59.7 (12.4) |
subtype1 | 24 | 58.7 (12.4) |
subtype2 | 54 | 60.2 (12.7) |
subtype3 | 20 | 59.4 (12.4) |
P value = 0.488 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 32 | 69 |
subtype1 | 6 | 21 |
subtype2 | 19 | 35 |
subtype3 | 7 | 13 |
P value = 0.311 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 21 | 87.6 (23.9) |
subtype1 | 4 | 97.5 (5.0) |
subtype2 | 12 | 90.0 (16.5) |
subtype3 | 5 | 74.0 (41.6) |
P value = 0.415 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 56 | 13 | 32 |
subtype1 | 15 | 5 | 7 |
subtype2 | 33 | 5 | 16 |
subtype3 | 8 | 3 | 9 |
P value = 0.451 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 20 | 11 | 4 |
subtype1 | 2 | 4 | 1 |
subtype2 | 10 | 4 | 1 |
subtype3 | 8 | 3 | 2 |
P value = 0.51 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 54 | 5 | 33 |
subtype1 | 11 | 1 | 11 |
subtype2 | 32 | 2 | 17 |
subtype3 | 11 | 2 | 5 |
P value = 0.297 (Chi-square test), Q value = 1
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 51 | 7 | 23 | 9 |
subtype1 | 14 | 2 | 3 | 3 |
subtype2 | 29 | 4 | 15 | 2 |
subtype3 | 8 | 1 | 5 | 4 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 21 | 26 | 38 |
P value = 0.15 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 78 | 12 | 0.0 - 182.7 (15.7) |
subtype1 | 19 | 4 | 0.0 - 80.8 (26.0) |
subtype2 | 25 | 6 | 0.2 - 182.7 (12.0) |
subtype3 | 34 | 2 | 0.0 - 129.9 (14.8) |
P value = 0.0523 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 82 | 60.0 (12.7) |
subtype1 | 20 | 65.8 (10.0) |
subtype2 | 25 | 59.4 (16.3) |
subtype3 | 37 | 57.3 (10.2) |
P value = 0.226 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 28 | 57 |
subtype1 | 6 | 15 |
subtype2 | 12 | 14 |
subtype3 | 10 | 28 |
P value = 0.144 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 20 | 92.0 (13.2) |
subtype1 | 6 | 81.7 (20.4) |
subtype2 | 1 | 100.0 (NA) |
subtype3 | 13 | 96.2 (5.1) |
P value = 6.37e-08 (Chi-square test), Q value = 3.7e-06
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 49 | 6 | 30 |
subtype1 | 15 | 0 | 6 |
subtype2 | 4 | 1 | 21 |
subtype3 | 30 | 5 | 3 |
P value = 0.142 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 20 | 9 | 4 |
subtype1 | 3 | 2 | 1 |
subtype2 | 9 | 7 | 3 |
subtype3 | 8 | 0 | 0 |
P value = 0.0567 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 45 | 4 | 33 |
subtype1 | 13 | 1 | 6 |
subtype2 | 16 | 3 | 7 |
subtype3 | 16 | 0 | 20 |
P value = 7.93e-06 (Chi-square test), Q value = 0.00045
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 46 | 5 | 22 | 8 |
subtype1 | 14 | 1 | 3 | 2 |
subtype2 | 4 | 1 | 15 | 6 |
subtype3 | 28 | 3 | 4 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 26 | 23 | 25 |
P value = 0.0277 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 71 | 13 | 0.5 - 182.7 (15.5) |
subtype1 | 24 | 3 | 0.5 - 54.9 (13.1) |
subtype2 | 22 | 8 | 0.9 - 93.3 (12.2) |
subtype3 | 25 | 2 | 6.4 - 182.7 (26.0) |
P value = 0.00648 (ANOVA), Q value = 0.32
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 71 | 59.7 (13.2) |
subtype1 | 24 | 56.5 (12.1) |
subtype2 | 22 | 55.8 (14.6) |
subtype3 | 25 | 66.3 (10.5) |
P value = 0.0242 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 22 | 52 |
subtype1 | 5 | 21 |
subtype2 | 12 | 11 |
subtype3 | 5 | 20 |
P value = 0.000102 (Chi-square test), Q value = 0.0055
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 38 | 9 | 27 |
subtype1 | 20 | 5 | 1 |
subtype2 | 5 | 2 | 16 |
subtype3 | 13 | 2 | 10 |
P value = 0.636 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 15 | 11 | 3 |
subtype1 | 2 | 0 | 0 |
subtype2 | 6 | 7 | 2 |
subtype3 | 7 | 4 | 1 |
P value = 0.0115 (Chi-square test), Q value = 0.56
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 46 | 5 | 16 |
subtype1 | 14 | 0 | 7 |
subtype2 | 12 | 5 | 5 |
subtype3 | 20 | 0 | 4 |
P value = 9.52e-05 (Chi-square test), Q value = 0.0052
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 35 | 3 | 20 | 8 |
subtype1 | 19 | 0 | 2 | 0 |
subtype2 | 4 | 1 | 9 | 7 |
subtype3 | 12 | 2 | 9 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 18 | 36 | 20 |
P value = 0.0127 (logrank test), Q value = 0.61
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 71 | 13 | 0.5 - 182.7 (15.5) |
subtype1 | 17 | 6 | 2.8 - 80.8 (10.8) |
subtype2 | 34 | 3 | 0.5 - 182.7 (13.8) |
subtype3 | 20 | 4 | 0.9 - 123.6 (25.2) |
P value = 0.454 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 71 | 59.7 (13.2) |
subtype1 | 17 | 57.3 (15.0) |
subtype2 | 34 | 59.3 (11.7) |
subtype3 | 20 | 62.6 (14.0) |
P value = 0.000595 (Fisher's exact test), Q value = 0.031
nPatients | FEMALE | MALE |
---|---|---|
ALL | 22 | 52 |
subtype1 | 11 | 7 |
subtype2 | 4 | 32 |
subtype3 | 7 | 13 |
P value = 0.578 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 86.4 (29.1) |
subtype1 | 3 | 93.3 (5.8) |
subtype2 | 7 | 95.7 (5.3) |
subtype3 | 1 | 0.0 (NA) |
P value = 0.000293 (Chi-square test), Q value = 0.016
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 38 | 9 | 27 |
subtype1 | 7 | 2 | 9 |
subtype2 | 26 | 6 | 4 |
subtype3 | 5 | 1 | 14 |
P value = 0.0583 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 15 | 11 | 3 |
subtype1 | 1 | 6 | 2 |
subtype2 | 4 | 1 | 0 |
subtype3 | 10 | 4 | 1 |
P value = 0.00397 (Chi-square test), Q value = 0.2
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 46 | 5 | 16 |
subtype1 | 9 | 4 | 4 |
subtype2 | 19 | 0 | 11 |
subtype3 | 18 | 1 | 1 |
P value = 2.81e-05 (Chi-square test), Q value = 0.0016
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 35 | 3 | 20 | 8 |
subtype1 | 6 | 1 | 3 | 6 |
subtype2 | 24 | 1 | 4 | 1 |
subtype3 | 5 | 1 | 13 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 34 | 36 | 31 |
P value = 0.582 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 94 | 14 | 0.0 - 182.7 (13.9) |
subtype1 | 33 | 4 | 0.0 - 96.9 (25.1) |
subtype2 | 34 | 7 | 0.2 - 182.7 (17.4) |
subtype3 | 27 | 3 | 0.0 - 123.6 (10.8) |
P value = 0.574 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 98 | 59.7 (12.4) |
subtype1 | 34 | 60.3 (12.5) |
subtype2 | 36 | 58.0 (14.4) |
subtype3 | 28 | 61.1 (9.5) |
P value = 0.178 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 32 | 69 |
subtype1 | 7 | 27 |
subtype2 | 15 | 21 |
subtype3 | 10 | 21 |
P value = 0.295 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 21 | 87.6 (23.9) |
subtype1 | 7 | 94.3 (5.3) |
subtype2 | 10 | 79.0 (32.8) |
subtype3 | 4 | 97.5 (5.0) |
P value = 0.137 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 56 | 13 | 32 |
subtype1 | 18 | 3 | 13 |
subtype2 | 19 | 3 | 14 |
subtype3 | 19 | 7 | 5 |
P value = 0.267 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 20 | 11 | 4 |
subtype1 | 9 | 3 | 1 |
subtype2 | 6 | 7 | 3 |
subtype3 | 5 | 1 | 0 |
P value = 0.266 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 54 | 5 | 33 |
subtype1 | 22 | 0 | 10 |
subtype2 | 19 | 4 | 13 |
subtype3 | 13 | 1 | 10 |
P value = 0.0296 (Chi-square test), Q value = 1
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 51 | 7 | 23 | 9 |
subtype1 | 17 | 3 | 12 | 0 |
subtype2 | 18 | 3 | 6 | 8 |
subtype3 | 16 | 1 | 5 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 21 | 40 | 40 |
P value = 0.693 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 94 | 14 | 0.0 - 182.7 (13.9) |
subtype1 | 19 | 2 | 0.0 - 123.6 (5.9) |
subtype2 | 36 | 7 | 0.2 - 182.7 (17.8) |
subtype3 | 39 | 5 | 0.0 - 96.9 (19.2) |
P value = 0.925 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 98 | 59.7 (12.4) |
subtype1 | 19 | 60.7 (9.8) |
subtype2 | 39 | 59.3 (13.8) |
subtype3 | 40 | 59.5 (12.4) |
P value = 0.0974 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 32 | 69 |
subtype1 | 7 | 14 |
subtype2 | 17 | 23 |
subtype3 | 8 | 32 |
P value = 0.647 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 21 | 87.6 (23.9) |
subtype1 | 3 | 96.7 (5.8) |
subtype2 | 11 | 89.1 (17.0) |
subtype3 | 7 | 81.4 (36.3) |
P value = 0.0183 (Chi-square test), Q value = 0.86
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 56 | 13 | 32 |
subtype1 | 14 | 6 | 1 |
subtype2 | 21 | 3 | 16 |
subtype3 | 21 | 4 | 15 |
P value = 0.262 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 20 | 11 | 4 |
subtype1 | 2 | 0 | 0 |
subtype2 | 7 | 7 | 3 |
subtype3 | 11 | 4 | 1 |
P value = 0.239 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 54 | 5 | 33 |
subtype1 | 10 | 0 | 7 |
subtype2 | 19 | 4 | 16 |
subtype3 | 25 | 1 | 10 |
P value = 0.0732 (Chi-square test), Q value = 1
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 51 | 7 | 23 | 9 |
subtype1 | 11 | 1 | 2 | 0 |
subtype2 | 20 | 3 | 8 | 8 |
subtype3 | 20 | 3 | 13 | 1 |
-
Cluster data file = KIRP-TP.mergedcluster.txt
-
Clinical data file = KIRP-TP.clin.merged.picked.txt
-
Number of patients = 101
-
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 continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between two tumor subtypes using 't.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 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 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 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.