(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 10 different clustering approaches and 8 clinical features across 502 patients, 35 significant findings detected with P value < 0.05 and Q value < 0.25.
-
CNMF clustering analysis on array-based mRNA expression data identified 3 subtypes that do not correlate to any clinical features.
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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 correlate to 'Time to Death', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
-
3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'Time to Death', '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', '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', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
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Consensus hierarchical 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'.
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CNMF clustering analysis on sequencing-based miR expression data identified 3 subtypes that correlate to 'Time to Death', 'GENDER', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
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Consensus hierarchical clustering analysis on sequencing-based miR expression data identified 3 subtypes that correlate to 'Time to Death' and 'PATHOLOGY.T'.
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 (1.00) |
0.795 (1.00) |
0.634 (1.00) |
0.00911 (0.357) |
0.0704 (1.00) |
0.12 (1.00) |
0.0134 (0.482) |
|
mRNA cHierClus subtypes |
0.422 (1.00) |
0.607 (1.00) |
0.82 (1.00) |
0.00779 (0.327) |
0.124 (1.00) |
0.0988 (1.00) |
0.0102 (0.388) |
|
CN CNMF |
0.000165 (0.00922) |
0.0782 (1.00) |
0.177 (1.00) |
0.889 (1.00) |
0.00196 (0.0923) |
0.0272 (0.924) |
0.000486 (0.0253) |
0.00154 (0.074) |
METHLYATION CNMF |
6.32e-06 (0.000392) |
0.00858 (0.352) |
0.00326 (0.147) |
0.134 (1.00) |
2.64e-10 (2.01e-08) |
0.147 (1.00) |
6.41e-05 (0.00378) |
3.89e-09 (2.92e-07) |
RPPA CNMF subtypes |
4.15e-07 (2.9e-05) |
0.127 (1.00) |
0.22 (1.00) |
0.552 (1.00) |
4.3e-06 (0.000279) |
0.149 (1.00) |
5.29e-06 (0.000333) |
9.71e-08 (7.09e-06) |
RPPA cHierClus subtypes |
7.29e-07 (5.03e-05) |
0.0772 (1.00) |
0.336 (1.00) |
0.0291 (0.961) |
1.02e-07 (7.34e-06) |
0.252 (1.00) |
0.000361 (0.0191) |
1.59e-07 (1.13e-05) |
RNAseq CNMF subtypes |
1.63e-06 (0.000109) |
0.09 (1.00) |
0.000154 (0.00878) |
0.66 (1.00) |
4.85e-06 (0.00031) |
0.0117 (0.433) |
0.000645 (0.0326) |
1.27e-06 (8.64e-05) |
RNAseq cHierClus subtypes |
3.34e-08 (2.47e-06) |
0.358 (1.00) |
0.00326 (0.147) |
0.357 (1.00) |
7.56e-12 (5.82e-10) |
0.000966 (0.0474) |
2e-06 (0.000132) |
2.63e-12 (2.05e-10) |
MIRseq CNMF subtypes |
8.12e-06 (0.000495) |
0.0537 (1.00) |
0.00265 (0.122) |
0.149 (1.00) |
0.00028 (0.0154) |
0.00693 (0.298) |
0.000305 (0.0164) |
8.11e-05 (0.0047) |
MIRseq cHierClus subtypes |
2.74e-05 (0.00165) |
0.0521 (1.00) |
0.182 (1.00) |
0.849 (1.00) |
0.00064 (0.0326) |
0.00892 (0.357) |
0.282 (1.00) |
0.0143 (0.501) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 34 | 24 | 14 |
P value = 0.231 (logrank test), Q value = 1
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), Q value = 1
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), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 29 | 43 |
subtype1 | 15 | 19 |
subtype2 | 10 | 14 |
subtype3 | 4 | 10 |
P value = 0.00911 (Chi-square test), Q value = 0.36
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), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 35 | 3 |
subtype1 | 18 | 0 |
subtype2 | 10 | 3 |
subtype3 | 7 | 0 |
P value = 0.12 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 |
---|---|---|
ALL | 67 | 5 |
subtype1 | 33 | 1 |
subtype2 | 20 | 4 |
subtype3 | 14 | 0 |
P value = 0.0134 (Chi-square test), Q value = 0.48
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), Q value = 1
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), Q value = 1
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), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 29 | 43 |
subtype1 | 5 | 10 |
subtype2 | 9 | 14 |
subtype3 | 15 | 19 |
P value = 0.00779 (Chi-square test), Q value = 0.33
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), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 35 | 3 |
subtype1 | 7 | 0 |
subtype2 | 11 | 3 |
subtype3 | 17 | 0 |
P value = 0.0988 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 |
---|---|---|
ALL | 67 | 5 |
subtype1 | 15 | 0 |
subtype2 | 19 | 4 |
subtype3 | 33 | 1 |
P value = 0.0102 (Chi-square test), Q value = 0.39
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), Q value = 0.0092
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), Q value = 1
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), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 171 | 322 |
subtype1 | 42 | 90 |
subtype2 | 78 | 119 |
subtype3 | 51 | 113 |
P value = 0.889 (ANOVA), Q value = 1
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), Q value = 0.092
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), Q value = 0.92
nPatients | 0 | 1 |
---|---|---|
ALL | 228 | 18 |
subtype1 | 55 | 5 |
subtype2 | 91 | 2 |
subtype3 | 82 | 11 |
P value = 0.000486 (Fisher's exact test), Q value = 0.025
nPatients | M0 | M1 |
---|---|---|
ALL | 417 | 76 |
subtype1 | 102 | 30 |
subtype2 | 181 | 16 |
subtype3 | 134 | 30 |
P value = 0.00154 (Chi-square test), Q value = 0.074
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), Q value = 0.00039
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), Q value = 0.35
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), Q value = 0.15
nPatients | FEMALE | MALE |
---|---|---|
ALL | 96 | 187 |
subtype1 | 21 | 76 |
subtype2 | 52 | 68 |
subtype3 | 23 | 43 |
P value = 0.134 (ANOVA), Q value = 1
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), Q value = 2e-08
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), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 127 | 9 |
subtype1 | 43 | 5 |
subtype2 | 54 | 1 |
subtype3 | 30 | 3 |
P value = 6.41e-05 (Fisher's exact test), Q value = 0.0038
nPatients | M0 | M1 |
---|---|---|
ALL | 232 | 51 |
subtype1 | 66 | 31 |
subtype2 | 109 | 11 |
subtype3 | 57 | 9 |
P value = 3.89e-09 (Chi-square test), Q value = 2.9e-07
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), Q value = 2.9e-05
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), Q value = 1
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), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 151 | 303 |
subtype1 | 45 | 115 |
subtype2 | 55 | 95 |
subtype3 | 51 | 93 |
P value = 0.552 (ANOVA), Q value = 1
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), Q value = 0.00028
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), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 208 | 16 |
subtype1 | 77 | 10 |
subtype2 | 60 | 2 |
subtype3 | 71 | 4 |
P value = 5.29e-06 (Fisher's exact test), Q value = 0.00033
nPatients | M0 | M1 |
---|---|---|
ALL | 380 | 74 |
subtype1 | 116 | 44 |
subtype2 | 139 | 11 |
subtype3 | 125 | 19 |
P value = 9.71e-08 (Chi-square test), Q value = 7.1e-06
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), Q value = 5e-05
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), Q value = 1
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), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 151 | 303 |
subtype1 | 39 | 93 |
subtype2 | 79 | 136 |
subtype3 | 33 | 74 |
P value = 0.0291 (ANOVA), Q value = 0.96
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), Q value = 7.3e-06
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), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 208 | 16 |
subtype1 | 66 | 4 |
subtype2 | 82 | 4 |
subtype3 | 60 | 8 |
P value = 0.000361 (Fisher's exact test), Q value = 0.019
nPatients | M0 | M1 |
---|---|---|
ALL | 380 | 74 |
subtype1 | 113 | 19 |
subtype2 | 191 | 24 |
subtype3 | 76 | 31 |
P value = 1.59e-07 (Chi-square test), Q value = 1.1e-05
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 | 199 | 180 | 101 |
P value = 1.63e-06 (logrank test), Q value = 0.00011
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 478 | 155 | 0.1 - 111.0 (34.3) |
subtype1 | 199 | 44 | 0.1 - 111.0 (37.0) |
subtype2 | 179 | 83 | 0.1 - 90.3 (30.6) |
subtype3 | 100 | 28 | 0.1 - 93.3 (35.2) |
P value = 0.09 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 479 | 60.6 (12.2) |
subtype1 | 198 | 61.7 (12.2) |
subtype2 | 180 | 60.6 (11.8) |
subtype3 | 101 | 58.4 (12.7) |
P value = 0.000154 (Fisher's exact test), Q value = 0.0088
nPatients | FEMALE | MALE |
---|---|---|
ALL | 167 | 313 |
subtype1 | 90 | 109 |
subtype2 | 45 | 135 |
subtype3 | 32 | 69 |
P value = 0.66 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 34 | 90.9 (17.8) |
subtype1 | 14 | 91.4 (8.6) |
subtype2 | 12 | 87.5 (28.3) |
subtype3 | 8 | 95.0 (7.6) |
P value = 4.85e-06 (Chi-square test), Q value = 0.00031
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 238 | 60 | 171 | 11 |
subtype1 | 118 | 22 | 57 | 2 |
subtype2 | 59 | 27 | 88 | 6 |
subtype3 | 61 | 11 | 26 | 3 |
P value = 0.0117 (Fisher's exact test), Q value = 0.43
nPatients | 0 | 1 |
---|---|---|
ALL | 228 | 17 |
subtype1 | 96 | 2 |
subtype2 | 85 | 12 |
subtype3 | 47 | 3 |
P value = 0.000645 (Fisher's exact test), Q value = 0.033
nPatients | M0 | M1 |
---|---|---|
ALL | 403 | 77 |
subtype1 | 176 | 23 |
subtype2 | 136 | 44 |
subtype3 | 91 | 10 |
P value = 1.27e-06 (Chi-square test), Q value = 8.6e-05
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 234 | 48 | 117 | 81 |
subtype1 | 118 | 18 | 39 | 24 |
subtype2 | 56 | 21 | 58 | 45 |
subtype3 | 60 | 9 | 20 | 12 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 73 | 215 | 192 |
P value = 3.34e-08 (logrank test), Q value = 2.5e-06
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 478 | 155 | 0.1 - 111.0 (34.3) |
subtype1 | 72 | 14 | 0.2 - 92.0 (27.8) |
subtype2 | 214 | 48 | 0.1 - 111.0 (37.2) |
subtype3 | 192 | 93 | 0.1 - 93.3 (30.5) |
P value = 0.358 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 479 | 60.6 (12.2) |
subtype1 | 73 | 58.7 (13.2) |
subtype2 | 214 | 61.0 (12.4) |
subtype3 | 192 | 60.8 (11.5) |
P value = 0.00326 (Fisher's exact test), Q value = 0.15
nPatients | FEMALE | MALE |
---|---|---|
ALL | 167 | 313 |
subtype1 | 23 | 50 |
subtype2 | 92 | 123 |
subtype3 | 52 | 140 |
P value = 0.357 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 34 | 90.9 (17.8) |
subtype1 | 10 | 95.0 (9.7) |
subtype2 | 13 | 93.1 (6.3) |
subtype3 | 11 | 84.5 (29.1) |
P value = 7.56e-12 (Chi-square test), Q value = 5.8e-10
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 238 | 60 | 171 | 11 |
subtype1 | 55 | 6 | 11 | 1 |
subtype2 | 126 | 27 | 61 | 1 |
subtype3 | 57 | 27 | 99 | 9 |
P value = 0.000966 (Fisher's exact test), Q value = 0.047
nPatients | 0 | 1 |
---|---|---|
ALL | 228 | 17 |
subtype1 | 32 | 2 |
subtype2 | 104 | 1 |
subtype3 | 92 | 14 |
P value = 2e-06 (Fisher's exact test), Q value = 0.00013
nPatients | M0 | M1 |
---|---|---|
ALL | 403 | 77 |
subtype1 | 70 | 3 |
subtype2 | 191 | 24 |
subtype3 | 142 | 50 |
P value = 2.63e-12 (Chi-square test), Q value = 2.1e-10
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 234 | 48 | 117 | 81 |
subtype1 | 54 | 6 | 10 | 3 |
subtype2 | 126 | 21 | 43 | 25 |
subtype3 | 54 | 21 | 64 | 53 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 209 | 106 | 165 |
P value = 8.12e-06 (logrank test), Q value = 5e-04
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), Q value = 1
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), Q value = 0.12
nPatients | FEMALE | MALE |
---|---|---|
ALL | 163 | 317 |
subtype1 | 88 | 121 |
subtype2 | 33 | 73 |
subtype3 | 42 | 123 |
P value = 0.149 (ANOVA), Q value = 1
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), Q value = 0.015
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), Q value = 0.3
nPatients | 0 | 1 |
---|---|---|
ALL | 222 | 17 |
subtype1 | 95 | 2 |
subtype2 | 51 | 3 |
subtype3 | 76 | 12 |
P value = 0.000305 (Fisher's exact test), Q value = 0.016
nPatients | M0 | M1 |
---|---|---|
ALL | 405 | 75 |
subtype1 | 184 | 25 |
subtype2 | 97 | 9 |
subtype3 | 124 | 41 |
P value = 8.11e-05 (Chi-square test), Q value = 0.0047
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), Q value = 0.0016
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), Q value = 1
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), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 163 | 317 |
subtype1 | 15 | 36 |
subtype2 | 105 | 176 |
subtype3 | 43 | 105 |
P value = 0.849 (ANOVA), Q value = 1
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), Q value = 0.033
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), Q value = 0.36
nPatients | 0 | 1 |
---|---|---|
ALL | 222 | 17 |
subtype1 | 26 | 5 |
subtype2 | 128 | 4 |
subtype3 | 68 | 8 |
P value = 0.282 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 |
---|---|---|
ALL | 405 | 75 |
subtype1 | 45 | 6 |
subtype2 | 241 | 40 |
subtype3 | 119 | 29 |
P value = 0.0143 (Chi-square test), Q value = 0.5
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 |
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Cluster data file = KIRC-TP.mergedcluster.txt
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Clinical data file = KIRC-TP.clin.merged.picked.txt
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Number of patients = 502
-
Number of clustering approaches = 10
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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
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.