This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 10 different clustering approaches and 8 clinical features across 502 patients, 47 significant findings detected with P value < 0.05.
-
CNMF clustering analysis on array-based mRNA expression data identified 3 subtypes that correlate to 'PATHOLOGY.T' and 'TUMOR.STAGE'.
-
Consensus hierarchical clustering analysis on array-based mRNA expression data identified 3 subtypes that correlate to 'PATHOLOGY.T' and 'TUMOR.STAGE'.
-
3 subtypes identified in current cancer cohort by 'CN CNMF'. These subtypes correlate to 'Time to Death', 'PATHOLOGY.T', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
-
3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'Time to Death', 'AGE', 'GENDER', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
-
CNMF clustering analysis on RPPA data identified 3 subtypes that correlate to 'Time to Death', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
-
Consensus hierarchical clustering analysis on RPPA data identified 3 subtypes that correlate to 'Time to Death', 'KARNOFSKY.PERFORMANCE.SCORE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
-
CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'Time to Death', 'GENDER', 'PATHOLOGY.T', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
-
Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'Time to Death', 'AGE', 'GENDER', 'PATHOLOGY.T', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
-
CNMF clustering analysis on sequencing-based miR expression data identified 3 subtypes that correlate to 'Time to Death', 'GENDER', 'PATHOLOGY.T', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
-
Consensus hierarchical clustering analysis on sequencing-based miR expression data identified 3 subtypes that correlate to 'Time to Death', 'PATHOLOGY.T', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
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 | Fisher's exact test | Fisher's exact test | Chi-square test |
mRNA CNMF subtypes | 0.231 | 0.795 | 0.634 | 0.00911 | 0.0704 | 0.12 | 0.0134 | |
mRNA cHierClus subtypes | 0.422 | 0.607 | 0.82 | 0.00779 | 0.124 | 0.0988 | 0.0102 | |
CN CNMF | 0.000165 | 0.0782 | 0.177 | 0.889 | 0.00196 | 0.0272 | 0.000486 | 0.00154 |
METHLYATION CNMF | 6.32e-06 | 0.00858 | 0.00326 | 0.134 | 2.64e-10 | 0.147 | 6.41e-05 | 3.89e-09 |
RPPA CNMF subtypes | 4.15e-07 | 0.127 | 0.22 | 0.552 | 4.3e-06 | 0.149 | 5.29e-06 | 9.71e-08 |
RPPA cHierClus subtypes | 7.29e-07 | 0.0772 | 0.336 | 0.0291 | 1.02e-07 | 0.252 | 0.000361 | 1.59e-07 |
RNAseq CNMF subtypes | 1.69e-07 | 0.265 | 1.03e-05 | 0.709 | 2.57e-06 | 0.016 | 7.98e-05 | 4.97e-07 |
RNAseq cHierClus subtypes | 1.36e-08 | 0.0383 | 0.00211 | 0.351 | 1.13e-12 | 0.00226 | 3.74e-06 | 5.72e-13 |
MIRseq CNMF subtypes | 8.12e-06 | 0.0537 | 0.00265 | 0.149 | 0.00028 | 0.00693 | 0.000305 | 8.11e-05 |
MIRseq cHierClus subtypes | 2.74e-05 | 0.0521 | 0.182 | 0.849 | 0.00064 | 0.00892 | 0.282 | 0.0143 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 34 | 24 | 14 |
P value = 0.231 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 71 | 13 | 0.5 - 101.1 (32.6) |
subtype1 | 33 | 4 | 0.5 - 101.1 (31.0) |
subtype2 | 24 | 8 | 0.5 - 93.3 (36.7) |
subtype3 | 14 | 1 | 1.3 - 84.4 (25.0) |
P value = 0.795 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 71 | 60.5 (12.4) |
subtype1 | 33 | 60.2 (13.8) |
subtype2 | 24 | 59.9 (11.1) |
subtype3 | 14 | 62.6 (11.3) |
P value = 0.634 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 29 | 43 |
subtype1 | 15 | 19 |
subtype2 | 10 | 14 |
subtype3 | 4 | 10 |
P value = 0.00911 (Chi-square test)
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 41 | 14 | 17 |
subtype1 | 23 | 4 | 7 |
subtype2 | 10 | 4 | 10 |
subtype3 | 8 | 6 | 0 |
P value = 0.0704 (Fisher's exact test)
nPatients | 0 | 1 |
---|---|---|
ALL | 35 | 3 |
subtype1 | 18 | 0 |
subtype2 | 10 | 3 |
subtype3 | 7 | 0 |
P value = 0.12 (Fisher's exact test)
nPatients | M0 | M1 |
---|---|---|
ALL | 67 | 5 |
subtype1 | 33 | 1 |
subtype2 | 20 | 4 |
subtype3 | 14 | 0 |
P value = 0.0134 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 40 | 15 | 12 | 5 |
subtype1 | 23 | 5 | 5 | 1 |
subtype2 | 9 | 4 | 7 | 4 |
subtype3 | 8 | 6 | 0 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 15 | 23 | 34 |
P value = 0.422 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 71 | 13 | 0.5 - 101.1 (32.6) |
subtype1 | 15 | 2 | 1.3 - 84.4 (24.2) |
subtype2 | 23 | 7 | 0.5 - 93.3 (36.8) |
subtype3 | 33 | 4 | 0.5 - 101.1 (31.0) |
P value = 0.607 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 71 | 60.5 (12.4) |
subtype1 | 15 | 63.2 (11.2) |
subtype2 | 23 | 59.1 (10.7) |
subtype3 | 33 | 60.4 (14.0) |
P value = 0.82 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 29 | 43 |
subtype1 | 5 | 10 |
subtype2 | 9 | 14 |
subtype3 | 15 | 19 |
P value = 0.00779 (Chi-square test)
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 41 | 14 | 17 |
subtype1 | 9 | 6 | 0 |
subtype2 | 9 | 4 | 10 |
subtype3 | 23 | 4 | 7 |
P value = 0.124 (Fisher's exact test)
nPatients | 0 | 1 |
---|---|---|
ALL | 35 | 3 |
subtype1 | 7 | 0 |
subtype2 | 11 | 3 |
subtype3 | 17 | 0 |
P value = 0.0988 (Fisher's exact test)
nPatients | M0 | M1 |
---|---|---|
ALL | 67 | 5 |
subtype1 | 15 | 0 |
subtype2 | 19 | 4 |
subtype3 | 33 | 1 |
P value = 0.0102 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 40 | 15 | 12 | 5 |
subtype1 | 9 | 6 | 0 | 0 |
subtype2 | 8 | 4 | 7 | 4 |
subtype3 | 23 | 5 | 5 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 132 | 197 | 164 |
P value = 0.000165 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 490 | 158 | 0.1 - 111.0 (35.2) |
subtype1 | 132 | 50 | 0.2 - 97.5 (36.6) |
subtype2 | 195 | 43 | 0.1 - 111.0 (37.5) |
subtype3 | 163 | 65 | 0.1 - 109.9 (28.5) |
P value = 0.0782 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 492 | 60.6 (12.2) |
subtype1 | 131 | 62.5 (11.8) |
subtype2 | 197 | 59.5 (12.7) |
subtype3 | 164 | 60.3 (11.7) |
P value = 0.177 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 171 | 322 |
subtype1 | 42 | 90 |
subtype2 | 78 | 119 |
subtype3 | 51 | 113 |
P value = 0.889 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 88.3 (23.0) |
subtype1 | 14 | 88.6 (26.0) |
subtype2 | 9 | 91.1 (10.5) |
subtype3 | 13 | 86.2 (26.9) |
P value = 0.00196 (Chi-square test)
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 242 | 64 | 176 | 11 |
subtype1 | 54 | 19 | 57 | 2 |
subtype2 | 116 | 25 | 55 | 1 |
subtype3 | 72 | 20 | 64 | 8 |
P value = 0.0272 (Fisher's exact test)
nPatients | 0 | 1 |
---|---|---|
ALL | 228 | 18 |
subtype1 | 55 | 5 |
subtype2 | 91 | 2 |
subtype3 | 82 | 11 |
P value = 0.000486 (Fisher's exact test)
nPatients | M0 | M1 |
---|---|---|
ALL | 417 | 76 |
subtype1 | 102 | 30 |
subtype2 | 181 | 16 |
subtype3 | 134 | 30 |
P value = 0.00154 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 238 | 52 | 123 | 80 |
subtype1 | 52 | 16 | 33 | 31 |
subtype2 | 116 | 19 | 45 | 17 |
subtype3 | 70 | 17 | 45 | 32 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 97 | 120 | 66 |
P value = 6.32e-06 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 281 | 95 | 0.1 - 109.9 (28.5) |
subtype1 | 96 | 49 | 0.2 - 84.7 (28.6) |
subtype2 | 119 | 21 | 0.1 - 109.6 (31.5) |
subtype3 | 66 | 25 | 0.1 - 109.9 (21.3) |
P value = 0.00858 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 283 | 61.5 (12.0) |
subtype1 | 97 | 63.6 (10.2) |
subtype2 | 120 | 59.0 (12.9) |
subtype3 | 66 | 63.0 (11.9) |
P value = 0.00326 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 96 | 187 |
subtype1 | 21 | 76 |
subtype2 | 52 | 68 |
subtype3 | 23 | 43 |
P value = 0.134 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 28 | 92.5 (8.0) |
subtype1 | 6 | 88.3 (7.5) |
subtype2 | 17 | 92.4 (8.3) |
subtype3 | 5 | 98.0 (4.5) |
P value = 2.64e-10 (Chi-square test)
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 132 | 36 | 107 | 8 |
subtype1 | 20 | 14 | 59 | 4 |
subtype2 | 78 | 18 | 24 | 0 |
subtype3 | 34 | 4 | 24 | 4 |
P value = 0.147 (Fisher's exact test)
nPatients | 0 | 1 |
---|---|---|
ALL | 127 | 9 |
subtype1 | 43 | 5 |
subtype2 | 54 | 1 |
subtype3 | 30 | 3 |
P value = 6.41e-05 (Fisher's exact test)
nPatients | M0 | M1 |
---|---|---|
ALL | 232 | 51 |
subtype1 | 66 | 31 |
subtype2 | 109 | 11 |
subtype3 | 57 | 9 |
P value = 3.89e-09 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 130 | 24 | 73 | 56 |
subtype1 | 20 | 9 | 35 | 33 |
subtype2 | 78 | 12 | 19 | 11 |
subtype3 | 32 | 3 | 19 | 12 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 160 | 150 | 144 |
P value = 4.15e-07 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 452 | 151 | 0.1 - 111.0 (34.3) |
subtype1 | 158 | 75 | 0.2 - 97.5 (30.6) |
subtype2 | 150 | 29 | 0.3 - 111.0 (38.3) |
subtype3 | 144 | 47 | 0.1 - 96.8 (30.2) |
P value = 0.127 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 60.4 (12.3) |
subtype1 | 160 | 61.9 (12.1) |
subtype2 | 149 | 60.2 (12.7) |
subtype3 | 144 | 59.0 (12.0) |
P value = 0.22 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 151 | 303 |
subtype1 | 45 | 115 |
subtype2 | 55 | 95 |
subtype3 | 51 | 93 |
P value = 0.552 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 34 | 93.5 (7.7) |
subtype1 | 9 | 91.1 (7.8) |
subtype2 | 15 | 94.7 (8.3) |
subtype3 | 10 | 94.0 (7.0) |
P value = 4.3e-06 (Chi-square test)
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 224 | 54 | 165 | 11 |
subtype1 | 51 | 24 | 77 | 8 |
subtype2 | 93 | 13 | 43 | 1 |
subtype3 | 80 | 17 | 45 | 2 |
P value = 0.149 (Fisher's exact test)
nPatients | 0 | 1 |
---|---|---|
ALL | 208 | 16 |
subtype1 | 77 | 10 |
subtype2 | 60 | 2 |
subtype3 | 71 | 4 |
P value = 5.29e-06 (Fisher's exact test)
nPatients | M0 | M1 |
---|---|---|
ALL | 380 | 74 |
subtype1 | 116 | 44 |
subtype2 | 139 | 11 |
subtype3 | 125 | 19 |
P value = 9.71e-08 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 219 | 43 | 114 | 78 |
subtype1 | 49 | 18 | 46 | 47 |
subtype2 | 92 | 10 | 37 | 11 |
subtype3 | 78 | 15 | 31 | 20 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 132 | 215 | 107 |
P value = 7.29e-07 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 452 | 151 | 0.1 - 111.0 (34.3) |
subtype1 | 132 | 43 | 0.2 - 111.0 (36.6) |
subtype2 | 215 | 53 | 0.1 - 96.8 (37.0) |
subtype3 | 105 | 55 | 0.1 - 91.4 (21.2) |
P value = 0.0772 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 60.4 (12.3) |
subtype1 | 131 | 61.9 (12.0) |
subtype2 | 215 | 59.1 (12.9) |
subtype3 | 107 | 61.4 (11.3) |
P value = 0.336 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 151 | 303 |
subtype1 | 39 | 93 |
subtype2 | 79 | 136 |
subtype3 | 33 | 74 |
P value = 0.0291 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 34 | 93.5 (7.7) |
subtype1 | 10 | 89.0 (8.8) |
subtype2 | 18 | 96.7 (4.9) |
subtype3 | 6 | 91.7 (9.8) |
P value = 1.02e-07 (Chi-square test)
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 224 | 54 | 165 | 11 |
subtype1 | 55 | 19 | 57 | 1 |
subtype2 | 135 | 20 | 58 | 2 |
subtype3 | 34 | 15 | 50 | 8 |
P value = 0.252 (Fisher's exact test)
nPatients | 0 | 1 |
---|---|---|
ALL | 208 | 16 |
subtype1 | 66 | 4 |
subtype2 | 82 | 4 |
subtype3 | 60 | 8 |
P value = 0.000361 (Fisher's exact test)
nPatients | M0 | M1 |
---|---|---|
ALL | 380 | 74 |
subtype1 | 113 | 19 |
subtype2 | 191 | 24 |
subtype3 | 76 | 31 |
P value = 1.59e-07 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 219 | 43 | 114 | 78 |
subtype1 | 53 | 15 | 43 | 21 |
subtype2 | 133 | 17 | 42 | 23 |
subtype3 | 33 | 11 | 29 | 34 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 196 | 177 | 96 |
P value = 1.69e-07 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 467 | 155 | 0.1 - 111.0 (34.3) |
subtype1 | 196 | 44 | 0.1 - 111.0 (37.0) |
subtype2 | 176 | 85 | 0.1 - 90.3 (29.1) |
subtype3 | 95 | 26 | 0.1 - 93.3 (36.5) |
P value = 0.265 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 468 | 60.6 (12.2) |
subtype1 | 195 | 61.4 (12.3) |
subtype2 | 177 | 60.5 (11.8) |
subtype3 | 96 | 59.0 (12.5) |
P value = 1.03e-05 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 162 | 307 |
subtype1 | 91 | 105 |
subtype2 | 41 | 136 |
subtype3 | 30 | 66 |
P value = 0.709 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 31 | 91.0 (18.7) |
subtype1 | 14 | 92.1 (8.9) |
subtype2 | 10 | 87.0 (31.3) |
subtype3 | 7 | 94.3 (7.9) |
P value = 2.57e-06 (Chi-square test)
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 228 | 59 | 171 | 11 |
subtype1 | 113 | 22 | 59 | 2 |
subtype2 | 56 | 26 | 89 | 6 |
subtype3 | 59 | 11 | 23 | 3 |
P value = 0.016 (Fisher's exact test)
nPatients | 0 | 1 |
---|---|---|
ALL | 224 | 17 |
subtype1 | 95 | 2 |
subtype2 | 85 | 12 |
subtype3 | 44 | 3 |
P value = 7.98e-05 (Fisher's exact test)
nPatients | M0 | M1 |
---|---|---|
ALL | 392 | 77 |
subtype1 | 173 | 23 |
subtype2 | 131 | 46 |
subtype3 | 88 | 8 |
P value = 4.97e-07 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 224 | 47 | 117 | 81 |
subtype1 | 113 | 18 | 41 | 24 |
subtype2 | 53 | 20 | 57 | 47 |
subtype3 | 58 | 9 | 19 | 10 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 200 | 72 | 197 |
P value = 1.36e-08 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 467 | 155 | 0.1 - 111.0 (34.3) |
subtype1 | 199 | 47 | 0.1 - 111.0 (38.7) |
subtype2 | 71 | 13 | 0.2 - 92.0 (34.3) |
subtype3 | 197 | 95 | 0.1 - 93.3 (29.0) |
P value = 0.0383 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 468 | 60.6 (12.2) |
subtype1 | 199 | 61.6 (12.4) |
subtype2 | 72 | 57.3 (12.7) |
subtype3 | 197 | 60.8 (11.6) |
P value = 0.00211 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 162 | 307 |
subtype1 | 87 | 113 |
subtype2 | 21 | 51 |
subtype3 | 54 | 143 |
P value = 0.351 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 31 | 91.0 (18.7) |
subtype1 | 12 | 93.3 (6.5) |
subtype2 | 10 | 95.0 (9.7) |
subtype3 | 9 | 83.3 (32.4) |
P value = 1.13e-12 (Chi-square test)
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 228 | 59 | 171 | 11 |
subtype1 | 115 | 25 | 59 | 1 |
subtype2 | 56 | 6 | 9 | 1 |
subtype3 | 57 | 28 | 103 | 9 |
P value = 0.00226 (Fisher's exact test)
nPatients | 0 | 1 |
---|---|---|
ALL | 224 | 17 |
subtype1 | 96 | 1 |
subtype2 | 29 | 2 |
subtype3 | 99 | 14 |
P value = 3.74e-06 (Fisher's exact test)
nPatients | M0 | M1 |
---|---|---|
ALL | 392 | 77 |
subtype1 | 177 | 23 |
subtype2 | 69 | 3 |
subtype3 | 146 | 51 |
P value = 5.72e-13 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 224 | 47 | 117 | 81 |
subtype1 | 115 | 19 | 42 | 24 |
subtype2 | 55 | 6 | 8 | 3 |
subtype3 | 54 | 22 | 67 | 54 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 209 | 106 | 165 |
P value = 8.12e-06 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 478 | 155 | 0.1 - 111.0 (35.2) |
subtype1 | 209 | 47 | 0.1 - 111.0 (36.2) |
subtype2 | 106 | 30 | 0.1 - 109.9 (35.8) |
subtype3 | 163 | 78 | 0.2 - 93.3 (31.1) |
P value = 0.0537 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 480 | 60.6 (12.2) |
subtype1 | 209 | 62.0 (12.2) |
subtype2 | 106 | 58.7 (12.7) |
subtype3 | 165 | 59.9 (11.7) |
P value = 0.00265 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 163 | 317 |
subtype1 | 88 | 121 |
subtype2 | 33 | 73 |
subtype3 | 42 | 123 |
P value = 0.149 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 88.3 (23.0) |
subtype1 | 16 | 91.9 (8.3) |
subtype2 | 9 | 95.6 (7.3) |
subtype3 | 11 | 77.3 (38.8) |
P value = 0.00028 (Chi-square test)
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 233 | 62 | 174 | 11 |
subtype1 | 115 | 26 | 66 | 2 |
subtype2 | 62 | 8 | 32 | 4 |
subtype3 | 56 | 28 | 76 | 5 |
P value = 0.00693 (Fisher's exact test)
nPatients | 0 | 1 |
---|---|---|
ALL | 222 | 17 |
subtype1 | 95 | 2 |
subtype2 | 51 | 3 |
subtype3 | 76 | 12 |
P value = 0.000305 (Fisher's exact test)
nPatients | M0 | M1 |
---|---|---|
ALL | 405 | 75 |
subtype1 | 184 | 25 |
subtype2 | 97 | 9 |
subtype3 | 124 | 41 |
P value = 8.11e-05 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 229 | 50 | 122 | 79 |
subtype1 | 114 | 20 | 49 | 26 |
subtype2 | 60 | 8 | 28 | 10 |
subtype3 | 55 | 22 | 45 | 43 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 51 | 281 | 148 |
P value = 2.74e-05 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 478 | 155 | 0.1 - 111.0 (35.2) |
subtype1 | 50 | 16 | 0.5 - 93.3 (39.6) |
subtype2 | 280 | 70 | 0.1 - 111.0 (36.0) |
subtype3 | 148 | 69 | 0.1 - 109.9 (29.5) |
P value = 0.0521 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 480 | 60.6 (12.2) |
subtype1 | 51 | 56.7 (12.1) |
subtype2 | 281 | 61.1 (11.9) |
subtype3 | 148 | 61.0 (12.6) |
P value = 0.182 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 163 | 317 |
subtype1 | 15 | 36 |
subtype2 | 105 | 176 |
subtype3 | 43 | 105 |
P value = 0.849 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 88.3 (23.0) |
subtype1 | 4 | 92.5 (9.6) |
subtype2 | 19 | 86.3 (22.4) |
subtype3 | 13 | 90.0 (27.4) |
P value = 0.00064 (Chi-square test)
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 233 | 62 | 174 | 11 |
subtype1 | 22 | 12 | 15 | 2 |
subtype2 | 153 | 35 | 91 | 2 |
subtype3 | 58 | 15 | 68 | 7 |
P value = 0.00892 (Fisher's exact test)
nPatients | 0 | 1 |
---|---|---|
ALL | 222 | 17 |
subtype1 | 26 | 5 |
subtype2 | 128 | 4 |
subtype3 | 68 | 8 |
P value = 0.282 (Fisher's exact test)
nPatients | M0 | M1 |
---|---|---|
ALL | 405 | 75 |
subtype1 | 45 | 6 |
subtype2 | 241 | 40 |
subtype3 | 119 | 29 |
P value = 0.0143 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 229 | 50 | 122 | 79 |
subtype1 | 22 | 10 | 13 | 6 |
subtype2 | 150 | 27 | 62 | 42 |
subtype3 | 57 | 13 | 47 | 31 |
-
Cluster data file = KIRC-TP.mergedcluster.txt
-
Clinical data file = KIRC-TP.clin.merged.picked.txt
-
Number of patients = 502
-
Number of clustering approaches = 10
-
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, one-way analysis of variance (Howell 2002) was applied to compare the clinical values between tumor subtypes using 'anova' 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
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.