(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, 33 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 'Copy Number Ratio CNMF subtypes'. 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 6 subtypes that correlate to 'Time to Death', 'PATHOLOGY.T', 'PATHOLOGY.N', '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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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 (0.382) |
0.0704 (1.00) |
0.12 (1.00) |
0.0134 (0.505) |
|
mRNA cHierClus subtypes |
0.422 (1.00) |
0.607 (1.00) |
0.82 (1.00) |
0.00779 (0.343) |
0.124 (1.00) |
0.0988 (1.00) |
0.0102 (0.409) |
|
Copy Number Ratio CNMF subtypes |
0.000165 (0.00939) |
0.0782 (1.00) |
0.177 (1.00) |
0.889 (1.00) |
0.00196 (0.0942) |
0.0272 (0.924) |
0.000486 (0.0272) |
0.00154 (0.0755) |
METHLYATION CNMF |
6.32e-06 (0.000392) |
0.00858 (0.369) |
0.00326 (0.153) |
0.134 (1.00) |
2.64e-10 (2.01e-08) |
0.147 (1.00) |
6.41e-05 (0.00384) |
3.89e-09 (2.88e-07) |
RPPA CNMF subtypes |
1.79e-09 (1.34e-07) |
0.129 (1.00) |
0.0891 (1.00) |
0.322 (1.00) |
9.52e-07 (6.38e-05) |
0.00106 (0.0532) |
3.89e-07 (2.72e-05) |
8e-09 (5.84e-07) |
RPPA cHierClus subtypes |
8.92e-08 (6.33e-06) |
0.00927 (0.382) |
0.578 (1.00) |
0.0463 (1.00) |
4.03e-07 (2.78e-05) |
0.253 (1.00) |
9.01e-05 (0.00532) |
6.23e-07 (4.24e-05) |
RNAseq CNMF subtypes |
1.63e-06 (0.000106) |
0.09 (1.00) |
0.000154 (0.00894) |
0.66 (1.00) |
4.85e-06 (0.000305) |
0.0117 (0.456) |
0.000645 (0.0342) |
1.27e-06 (8.38e-05) |
RNAseq cHierClus subtypes |
3.34e-08 (2.4e-06) |
0.358 (1.00) |
0.00326 (0.153) |
0.357 (1.00) |
7.56e-12 (5.82e-10) |
0.000966 (0.0493) |
2e-06 (0.000128) |
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 (0.924) |
0.000569 (0.0307) |
0.000534 (0.0294) |
MIRSEQ CHIERARCHICAL |
0.00618 (0.278) |
0.024 (0.841) |
0.249 (1.00) |
0.984 (1.00) |
0.0145 (0.523) |
0.0133 (0.505) |
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 = 0.38
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 = 0.51
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 = 0.34
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 = 0.41
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 = 0.0094
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 = 0.094
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 = 0.027
nPatients | M0 | M1 |
---|---|---|
ALL | 417 | 76 |
subtype1 | 102 | 30 |
subtype2 | 181 | 16 |
subtype3 | 134 | 30 |
P value = 0.00154 (Chi-square test), Q value = 0.076
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 = 0.37
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 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 101 | 90 | 86 | 76 | 44 | 57 |
P value = 1.79e-09 (logrank test), Q value = 1.3e-07
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 452 | 151 | 0.1 - 111.0 (34.3) |
subtype1 | 101 | 26 | 0.2 - 111.0 (43.7) |
subtype2 | 90 | 35 | 0.1 - 90.4 (29.4) |
subtype3 | 85 | 22 | 0.2 - 93.0 (35.3) |
subtype4 | 75 | 23 | 0.1 - 96.8 (27.9) |
subtype5 | 44 | 8 | 0.2 - 83.8 (36.5) |
subtype6 | 57 | 37 | 0.6 - 84.0 (19.7) |
P value = 0.129 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 60.4 (12.3) |
subtype1 | 100 | 61.8 (11.1) |
subtype2 | 90 | 58.0 (12.2) |
subtype3 | 86 | 62.3 (12.6) |
subtype4 | 76 | 60.0 (11.8) |
subtype5 | 44 | 58.3 (15.7) |
subtype6 | 57 | 61.2 (11.4) |
P value = 0.0891 (Chi-square test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 151 | 303 |
subtype1 | 43 | 58 |
subtype2 | 29 | 61 |
subtype3 | 28 | 58 |
subtype4 | 18 | 58 |
subtype5 | 18 | 26 |
subtype6 | 15 | 42 |
P value = 0.322 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 34 | 93.5 (7.7) |
subtype1 | 7 | 92.9 (7.6) |
subtype2 | 8 | 93.8 (5.2) |
subtype3 | 10 | 90.0 (9.4) |
subtype4 | 2 | 100.0 (0.0) |
subtype5 | 4 | 100.0 (0.0) |
subtype6 | 3 | 93.3 (11.5) |
P value = 9.52e-07 (Chi-square test), Q value = 6.4e-05
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 224 | 54 | 165 | 11 |
subtype1 | 54 | 15 | 31 | 1 |
subtype2 | 43 | 10 | 32 | 5 |
subtype3 | 41 | 12 | 33 | 0 |
subtype4 | 45 | 7 | 23 | 1 |
subtype5 | 33 | 2 | 9 | 0 |
subtype6 | 8 | 8 | 37 | 4 |
P value = 0.00106 (Chi-square test), Q value = 0.053
nPatients | 0 | 1 |
---|---|---|
ALL | 208 | 16 |
subtype1 | 48 | 1 |
subtype2 | 46 | 2 |
subtype3 | 43 | 2 |
subtype4 | 35 | 3 |
subtype5 | 13 | 0 |
subtype6 | 23 | 8 |
P value = 3.89e-07 (Chi-square test), Q value = 2.7e-05
nPatients | M0 | M1 |
---|---|---|
ALL | 380 | 74 |
subtype1 | 87 | 14 |
subtype2 | 71 | 19 |
subtype3 | 76 | 10 |
subtype4 | 68 | 8 |
subtype5 | 44 | 0 |
subtype6 | 34 | 23 |
P value = 8e-09 (Chi-square test), Q value = 5.8e-07
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 219 | 43 | 114 | 78 |
subtype1 | 54 | 10 | 22 | 15 |
subtype2 | 42 | 10 | 18 | 20 |
subtype3 | 39 | 11 | 26 | 10 |
subtype4 | 44 | 7 | 16 | 9 |
subtype5 | 33 | 2 | 9 | 0 |
subtype6 | 7 | 3 | 23 | 24 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 189 | 153 | 112 |
P value = 8.92e-08 (logrank test), Q value = 6.3e-06
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 452 | 151 | 0.1 - 111.0 (34.3) |
subtype1 | 189 | 42 | 0.1 - 96.8 (37.0) |
subtype2 | 153 | 50 | 0.2 - 111.0 (36.8) |
subtype3 | 110 | 59 | 0.1 - 91.4 (21.5) |
P value = 0.00927 (ANOVA), Q value = 0.38
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 60.4 (12.3) |
subtype1 | 189 | 58.4 (12.7) |
subtype2 | 152 | 62.3 (12.3) |
subtype3 | 112 | 61.3 (11.1) |
P value = 0.578 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 151 | 303 |
subtype1 | 68 | 121 |
subtype2 | 47 | 106 |
subtype3 | 36 | 76 |
P value = 0.0463 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 34 | 93.5 (7.7) |
subtype1 | 17 | 96.5 (4.9) |
subtype2 | 10 | 89.0 (8.8) |
subtype3 | 7 | 92.9 (9.5) |
P value = 4.03e-07 (Chi-square test), Q value = 2.8e-05
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 224 | 54 | 165 | 11 |
subtype1 | 120 | 19 | 48 | 2 |
subtype2 | 67 | 20 | 65 | 1 |
subtype3 | 37 | 15 | 52 | 8 |
P value = 0.253 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 208 | 16 |
subtype1 | 72 | 4 |
subtype2 | 76 | 4 |
subtype3 | 60 | 8 |
P value = 9.01e-05 (Fisher's exact test), Q value = 0.0053
nPatients | M0 | M1 |
---|---|---|
ALL | 380 | 74 |
subtype1 | 170 | 19 |
subtype2 | 131 | 22 |
subtype3 | 79 | 33 |
P value = 6.23e-07 (Chi-square test), Q value = 4.2e-05
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 219 | 43 | 114 | 78 |
subtype1 | 118 | 16 | 36 | 19 |
subtype2 | 65 | 16 | 48 | 24 |
subtype3 | 36 | 11 | 30 | 35 |
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 = 0.0089
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 = 0.46
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 = 8.4e-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 = 2.4e-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 = 0.049
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 = 0.92
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 = 0.84
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 = 0.52
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 = 0.51
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
-
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.