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, 32 significant findings detected with P value < 0.05 and Q value < 0.25.
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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.
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3 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes correlate to 'Time to Death', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
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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'.
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CNMF clustering analysis on RPPA data identified 3 subtypes that correlate to 'Time to Death', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
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Consensus hierarchical clustering analysis on RPPA data identified 3 subtypes that correlate to 'Time to Death', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
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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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4 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'Time to Death', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
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3 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes 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 | 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 (0.392) |
0.0704 (1.00) |
0.12 (1.00) |
0.0134 (0.532) |
|
mRNA cHierClus subtypes |
0.422 (1.00) |
0.607 (1.00) |
0.82 (1.00) |
0.00779 (0.351) |
0.124 (1.00) |
0.0988 (1.00) |
0.0102 (0.429) |
|
Copy Number Ratio CNMF subtypes |
0.000165 (0.00955) |
0.0782 (1.00) |
0.177 (1.00) |
0.889 (1.00) |
0.00196 (0.0962) |
0.0272 (0.979) |
0.000486 (0.0272) |
0.00154 (0.0771) |
METHLYATION CNMF |
6.32e-06 (0.000392) |
0.00858 (0.378) |
0.00326 (0.156) |
0.134 (1.00) |
2.64e-10 (2.01e-08) |
0.147 (1.00) |
6.41e-05 (0.00384) |
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 (0.991) |
1.02e-07 (7.34e-06) |
0.252 (1.00) |
0.000361 (0.0206) |
1.59e-07 (1.13e-05) |
RNAseq CNMF subtypes |
1.63e-06 (0.000109) |
0.09 (1.00) |
0.000154 (0.00909) |
0.66 (1.00) |
4.85e-06 (0.00031) |
0.0117 (0.48) |
0.000645 (0.0342) |
1.27e-06 (8.64e-05) |
RNAseq cHierClus subtypes |
3.34e-08 (2.47e-06) |
0.358 (1.00) |
0.00326 (0.156) |
0.357 (1.00) |
7.56e-12 (5.82e-10) |
0.000966 (0.0493) |
2e-06 (0.000132) |
2.63e-12 (2.05e-10) |
MIRSEQ CNMF |
9.84e-06 (6e-04) |
0.11 (1.00) |
0.0616 (1.00) |
0.255 (1.00) |
0.000675 (0.0351) |
0.0278 (0.979) |
0.000569 (0.0307) |
0.000534 (0.0294) |
MIRSEQ CHIERARCHICAL |
0.00618 (0.284) |
0.024 (0.889) |
0.249 (1.00) |
0.984 (1.00) |
0.0145 (0.552) |
0.0133 (0.532) |
0.76 (1.00) |
0.174 (1.00) |
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 = 0.39
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 = 0.53
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 = 0.35
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 = 0.43
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 = 0.0096
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 = 0.096
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 = 0.98
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 = 0.027
nPatients | M0 | M1 |
---|---|---|
ALL | 417 | 76 |
subtype1 | 102 | 30 |
subtype2 | 181 | 16 |
subtype3 | 134 | 30 |
P value = 0.00154 (Chi-square test), Q value = 0.077
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 = 0.38
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 = 0.16
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 = 0.99
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 = 0.021
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 = 0.0091
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 = 0.48
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 = 0.034
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 = 0.16
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 = 0.049
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 | 4 |
---|---|---|---|---|
Number of samples | 106 | 185 | 146 | 44 |
P value = 9.84e-06 (logrank test), Q value = 6e-04
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 479 | 156 | 0.1 - 111.0 (35.2) |
subtype1 | 106 | 30 | 0.1 - 109.9 (37.2) |
subtype2 | 185 | 41 | 0.1 - 111.0 (36.3) |
subtype3 | 144 | 69 | 0.2 - 93.3 (30.2) |
subtype4 | 44 | 16 | 0.1 - 84.7 (29.8) |
P value = 0.11 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 481 | 60.6 (12.2) |
subtype1 | 106 | 58.9 (12.4) |
subtype2 | 185 | 62.2 (12.4) |
subtype3 | 146 | 60.1 (11.7) |
subtype4 | 44 | 59.6 (11.7) |
P value = 0.0616 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 163 | 318 |
subtype1 | 36 | 70 |
subtype2 | 75 | 110 |
subtype3 | 39 | 107 |
subtype4 | 13 | 31 |
P value = 0.255 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 88.3 (23.0) |
subtype1 | 7 | 95.7 (7.9) |
subtype2 | 15 | 92.0 (8.6) |
subtype3 | 10 | 76.0 (40.6) |
subtype4 | 4 | 92.5 (5.0) |
P value = 0.000675 (Chi-square test), Q value = 0.035
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 233 | 62 | 175 | 11 |
subtype1 | 65 | 7 | 30 | 4 |
subtype2 | 100 | 24 | 59 | 2 |
subtype3 | 48 | 25 | 68 | 5 |
subtype4 | 20 | 6 | 18 | 0 |
P value = 0.0278 (Fisher's exact test), Q value = 0.98
nPatients | 0 | 1 |
---|---|---|
ALL | 222 | 18 |
subtype1 | 50 | 3 |
subtype2 | 83 | 2 |
subtype3 | 72 | 12 |
subtype4 | 17 | 1 |
P value = 0.000569 (Fisher's exact test), Q value = 0.031
nPatients | M0 | M1 |
---|---|---|
ALL | 405 | 76 |
subtype1 | 97 | 9 |
subtype2 | 164 | 21 |
subtype3 | 109 | 37 |
subtype4 | 35 | 9 |
P value = 0.000534 (Chi-square test), Q value = 0.029
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 229 | 50 | 122 | 80 |
subtype1 | 63 | 8 | 25 | 10 |
subtype2 | 100 | 19 | 43 | 23 |
subtype3 | 47 | 19 | 41 | 39 |
subtype4 | 19 | 4 | 13 | 8 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 167 | 261 | 53 |
P value = 0.00618 (logrank test), Q value = 0.28
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 479 | 156 | 0.1 - 111.0 (35.2) |
subtype1 | 167 | 70 | 0.1 - 109.9 (33.0) |
subtype2 | 260 | 70 | 0.1 - 111.0 (35.0) |
subtype3 | 52 | 16 | 0.2 - 93.3 (39.6) |
P value = 0.024 (ANOVA), Q value = 0.89
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 481 | 60.6 (12.2) |
subtype1 | 167 | 60.1 (12.3) |
subtype2 | 261 | 61.6 (12.1) |
subtype3 | 53 | 56.8 (11.3) |
P value = 0.249 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 163 | 318 |
subtype1 | 51 | 116 |
subtype2 | 97 | 164 |
subtype3 | 15 | 38 |
P value = 0.984 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 88.3 (23.0) |
subtype1 | 12 | 88.3 (28.2) |
subtype2 | 19 | 87.9 (22.7) |
subtype3 | 5 | 90.0 (10.0) |
P value = 0.0145 (Chi-square test), Q value = 0.55
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 233 | 62 | 175 | 11 |
subtype1 | 73 | 16 | 71 | 7 |
subtype2 | 137 | 34 | 88 | 2 |
subtype3 | 23 | 12 | 16 | 2 |
P value = 0.0133 (Fisher's exact test), Q value = 0.53
nPatients | 0 | 1 |
---|---|---|
ALL | 222 | 18 |
subtype1 | 70 | 9 |
subtype2 | 123 | 4 |
subtype3 | 29 | 5 |
P value = 0.76 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 |
---|---|---|
ALL | 405 | 76 |
subtype1 | 138 | 29 |
subtype2 | 221 | 40 |
subtype3 | 46 | 7 |
P value = 0.174 (Chi-square test), Q value = 1
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 229 | 50 | 122 | 80 |
subtype1 | 72 | 14 | 50 | 31 |
subtype2 | 134 | 26 | 59 | 42 |
subtype3 | 23 | 10 | 13 | 7 |
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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
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Number of clustering approaches = 10
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Number of selected clinical features = 8
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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.