This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 12 different clustering approaches and 12 clinical features across 533 patients, 66 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 correlate to 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', and 'RACE'.
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Consensus hierarchical clustering analysis on array-based mRNA expression data identified 7 subtypes that correlate to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', 'GENDER', and 'RACE'.
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3 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes correlate to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'GENDER', and 'RACE'.
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3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'Time to Death', 'YEARS_TO_BIRTH', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', 'GENDER', and 'RACE'.
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CNMF clustering analysis on RPPA data identified 6 subtypes that correlate to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'PATHOLOGY_M_STAGE'.
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Consensus hierarchical clustering analysis on RPPA data identified 3 subtypes that correlate to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', and 'PATHOLOGY_M_STAGE'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'GENDER', and 'RACE'.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 6 subtypes that correlate to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'GENDER', and 'RACE'.
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3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'Time to Death', 'YEARS_TO_BIRTH', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', and 'GENDER'.
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4 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes correlate to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'GENDER', and 'ETHNICITY'.
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4 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes correlate to 'Time to Death', 'GENDER', and 'RACE'.
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3 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes correlate to 'PATHOLOGY_T_STAGE', 'GENDER', and 'RACE'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
KARNOFSKY PERFORMANCE SCORE |
NUMBER PACK YEARS SMOKED |
YEAR OF TOBACCO SMOKING ONSET |
RACE | ETHNICITY |
Statistical Tests | logrank test | Kruskal-Wallis (anova) | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Kruskal-Wallis (anova) | Kruskal-Wallis (anova) | Kruskal-Wallis (anova) | Fisher's exact test | Fisher's exact test |
mRNA CNMF subtypes |
0.0843 (0.164) |
0.873 (1.00) |
0.00582 (0.0178) |
0.00784 (0.0226) |
0.0703 (0.141) |
0.121 (0.206) |
0.635 (0.832) |
0.0075 (0.022) |
0.317 (0.448) |
|||
mRNA cHierClus subtypes |
0.0254 (0.0589) |
0.168 (0.271) |
0.00051 (0.00193) |
0.00423 (0.0132) |
0.0993 (0.191) |
0.0109 (0.0296) |
5e-05 (0.000248) |
1e-05 (6.55e-05) |
0.472 (0.634) |
|||
Copy Number Ratio CNMF subtypes |
0.000804 (0.0029) |
0.0681 (0.139) |
3e-05 (0.00018) |
8e-05 (0.000372) |
0.0108 (0.0296) |
6e-05 (0.000288) |
0.0065 (0.0195) |
0.278 (0.405) |
0.475 (0.634) |
0.86 (1.00) |
0.017 (0.043) |
0.788 (0.97) |
METHLYATION CNMF |
4.23e-06 (6.55e-05) |
0.0178 (0.0434) |
1e-05 (6.55e-05) |
1e-05 (6.55e-05) |
0.25 (0.375) |
0.00014 (0.000611) |
2e-05 (0.000125) |
0.343 (0.47) |
0.762 (0.946) |
0.663 (0.844) |
0.0347 (0.0769) |
1 (1.00) |
RPPA CNMF subtypes |
1.65e-11 (1.19e-09) |
0.173 (0.273) |
1e-05 (6.55e-05) |
1e-05 (6.55e-05) |
0.0121 (0.0318) |
1e-05 (6.55e-05) |
0.102 (0.191) |
0.109 (0.196) |
0.112 (0.197) |
0.351 (0.476) |
||
RPPA cHierClus subtypes |
1.32e-13 (1.9e-11) |
0.111 (0.197) |
1e-05 (6.55e-05) |
1e-05 (6.55e-05) |
0.0527 (0.113) |
1e-05 (6.55e-05) |
0.105 (0.194) |
0.0648 (0.135) |
0.85 (1.00) |
0.0686 (0.139) |
||
RNAseq CNMF subtypes |
7.09e-07 (2.55e-05) |
0.143 (0.237) |
1e-05 (6.55e-05) |
1e-05 (6.55e-05) |
0.0127 (0.0326) |
0.00039 (0.00156) |
5e-05 (0.000248) |
0.315 (0.448) |
0.807 (0.977) |
0.858 (1.00) |
0.0195 (0.0468) |
0.107 (0.195) |
RNAseq cHierClus subtypes |
3.67e-08 (1.76e-06) |
0.119 (0.204) |
1e-05 (6.55e-05) |
1e-05 (6.55e-05) |
0.00399 (0.0128) |
5e-05 (0.000248) |
1e-05 (6.55e-05) |
0.278 (0.405) |
0.685 (0.865) |
0.00226 (0.00757) |
0.656 (0.844) |
|
MIRSEQ CNMF |
8.12e-06 (6.55e-05) |
0.0383 (0.0836) |
0.00023 (0.000946) |
0.0005 (0.00193) |
0.0114 (0.0303) |
0.00073 (0.0027) |
0.00226 (0.00757) |
0.908 (1.00) |
0.322 (0.45) |
1 (1.00) |
0.208 (0.319) |
0.181 (0.283) |
MIRSEQ CHIERARCHICAL |
0.000219 (0.000926) |
0.0794 (0.157) |
5e-05 (0.000248) |
9e-05 (0.000405) |
0.0202 (0.0476) |
5e-05 (0.000248) |
0.00114 (0.004) |
0.166 (0.271) |
0.807 (0.977) |
0.658 (0.844) |
0.13 (0.218) |
0.0175 (0.0434) |
MIRseq Mature CNMF subtypes |
0.00975 (0.0275) |
0.706 (0.884) |
0.305 (0.439) |
0.102 (0.191) |
0.2 (0.309) |
0.116 (0.201) |
0.0331 (0.0744) |
0.985 (1.00) |
1e-05 (6.55e-05) |
0.325 (0.45) |
||
MIRseq Mature cHierClus subtypes |
0.577 (0.763) |
0.0635 (0.135) |
0.24 (0.363) |
0.0285 (0.0652) |
0.169 (0.271) |
0.866 (1.00) |
0.00292 (0.00956) |
0.848 (1.00) |
1 (1.00) |
1e-05 (6.55e-05) |
0.276 (0.405) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 34 | 24 | 14 |
P value = 0.0843 (logrank test), Q value = 0.16
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 72 | 14 | 0.5 - 101.1 (36.6) |
subtype1 | 34 | 4 | 1.4 - 101.1 (32.0) |
subtype2 | 24 | 9 | 0.5 - 93.3 (38.2) |
subtype3 | 14 | 1 | 10.5 - 84.4 (38.8) |
P value = 0.873 (Kruskal-Wallis (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 = 0.00582 (Fisher's exact test), Q value = 0.018
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 40 | 13 | 14 | 5 |
subtype1 | 23 | 4 | 6 | 1 |
subtype2 | 9 | 3 | 8 | 4 |
subtype3 | 8 | 6 | 0 | 0 |
P value = 0.00784 (Fisher's exact test), Q value = 0.023
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 41 | 14 | 17 |
subtype1 | 23 | 4 | 7 |
subtype2 | 10 | 4 | 10 |
subtype3 | 8 | 6 | 0 |
P value = 0.0703 (Fisher's exact test), Q value = 0.14
nPatients | 0 | 1 |
---|---|---|
ALL | 35 | 3 |
subtype1 | 18 | 0 |
subtype2 | 10 | 3 |
subtype3 | 7 | 0 |
P value = 0.121 (Fisher's exact test), Q value = 0.21
nPatients | 0 | 1 |
---|---|---|
ALL | 67 | 5 |
subtype1 | 33 | 1 |
subtype2 | 20 | 4 |
subtype3 | 14 | 0 |
P value = 0.635 (Fisher's exact test), Q value = 0.83
nPatients | FEMALE | MALE |
---|---|---|
ALL | 29 | 43 |
subtype1 | 15 | 19 |
subtype2 | 10 | 14 |
subtype3 | 4 | 10 |
P value = 0.0075 (Fisher's exact test), Q value = 0.022
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 1 | 5 | 62 |
subtype1 | 0 | 0 | 32 |
subtype2 | 0 | 2 | 20 |
subtype3 | 1 | 3 | 10 |
P value = 0.317 (Fisher's exact test), Q value = 0.45
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 7 | 42 |
subtype1 | 5 | 19 |
subtype2 | 2 | 11 |
subtype3 | 0 | 12 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
---|---|---|---|---|---|---|---|
Number of samples | 12 | 12 | 4 | 11 | 13 | 9 | 11 |
P value = 0.0254 (logrank test), Q value = 0.059
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 72 | 14 | 0.5 - 101.1 (36.6) |
subtype1 | 12 | 1 | 12.3 - 47.2 (31.2) |
subtype2 | 12 | 2 | 0.5 - 90.3 (31.0) |
subtype3 | 4 | 2 | 1.7 - 37.6 (17.3) |
subtype4 | 11 | 6 | 14.2 - 93.3 (54.6) |
subtype5 | 13 | 3 | 11.1 - 101.1 (48.4) |
subtype6 | 9 | 0 | 1.4 - 59.8 (28.7) |
subtype7 | 11 | 0 | 12.1 - 84.4 (40.7) |
P value = 0.168 (Kruskal-Wallis (anova)), Q value = 0.27
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 71 | 60.5 (12.4) |
subtype1 | 11 | 63.3 (13.7) |
subtype2 | 12 | 62.2 (10.8) |
subtype3 | 4 | 57.2 (10.9) |
subtype4 | 11 | 56.2 (10.9) |
subtype5 | 13 | 64.1 (13.5) |
subtype6 | 9 | 50.7 (10.7) |
subtype7 | 11 | 65.4 (10.9) |
P value = 0.00051 (Fisher's exact test), Q value = 0.0019
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 40 | 13 | 14 | 5 |
subtype1 | 8 | 2 | 2 | 0 |
subtype2 | 8 | 2 | 2 | 0 |
subtype3 | 2 | 2 | 0 | 0 |
subtype4 | 0 | 1 | 6 | 4 |
subtype5 | 7 | 2 | 3 | 1 |
subtype6 | 8 | 0 | 1 | 0 |
subtype7 | 7 | 4 | 0 | 0 |
P value = 0.00423 (Fisher's exact test), Q value = 0.013
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 41 | 14 | 17 |
subtype1 | 8 | 2 | 2 |
subtype2 | 8 | 2 | 2 |
subtype3 | 2 | 2 | 0 |
subtype4 | 1 | 2 | 8 |
subtype5 | 7 | 2 | 4 |
subtype6 | 8 | 0 | 1 |
subtype7 | 7 | 4 | 0 |
P value = 0.0993 (Fisher's exact test), Q value = 0.19
nPatients | 0 | 1 |
---|---|---|
ALL | 35 | 3 |
subtype1 | 6 | 0 |
subtype2 | 5 | 0 |
subtype3 | 3 | 0 |
subtype4 | 5 | 3 |
subtype5 | 9 | 0 |
subtype6 | 3 | 0 |
subtype7 | 4 | 0 |
P value = 0.0109 (Fisher's exact test), Q value = 0.03
nPatients | 0 | 1 |
---|---|---|
ALL | 67 | 5 |
subtype1 | 12 | 0 |
subtype2 | 12 | 0 |
subtype3 | 4 | 0 |
subtype4 | 7 | 4 |
subtype5 | 12 | 1 |
subtype6 | 9 | 0 |
subtype7 | 11 | 0 |
P value = 5e-05 (Fisher's exact test), Q value = 0.00025
nPatients | FEMALE | MALE |
---|---|---|
ALL | 29 | 43 |
subtype1 | 0 | 12 |
subtype2 | 3 | 9 |
subtype3 | 1 | 3 |
subtype4 | 6 | 5 |
subtype5 | 12 | 1 |
subtype6 | 3 | 6 |
subtype7 | 4 | 7 |
P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 1 | 5 | 62 |
subtype1 | 0 | 0 | 11 |
subtype2 | 0 | 1 | 10 |
subtype3 | 1 | 3 | 0 |
subtype4 | 0 | 0 | 10 |
subtype5 | 0 | 0 | 13 |
subtype6 | 0 | 0 | 8 |
subtype7 | 0 | 1 | 10 |
P value = 0.472 (Fisher's exact test), Q value = 0.63
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 7 | 42 |
subtype1 | 1 | 7 |
subtype2 | 0 | 4 |
subtype3 | 0 | 2 |
subtype4 | 2 | 6 |
subtype5 | 3 | 7 |
subtype6 | 1 | 5 |
subtype7 | 0 | 11 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 237 | 133 | 154 |
P value = 0.000804 (logrank test), Q value = 0.0029
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 522 | 168 | 0.1 - 120.6 (36.4) |
subtype1 | 237 | 57 | 0.1 - 120.6 (37.0) |
subtype2 | 131 | 46 | 0.1 - 112.8 (38.6) |
subtype3 | 154 | 65 | 0.1 - 109.9 (31.3) |
P value = 0.0681 (Kruskal-Wallis (anova)), Q value = 0.14
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 523 | 60.6 (12.1) |
subtype1 | 237 | 60.0 (12.7) |
subtype2 | 133 | 59.7 (11.4) |
subtype3 | 153 | 62.4 (11.7) |
P value = 3e-05 (Fisher's exact test), Q value = 0.00018
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 260 | 57 | 127 | 80 |
subtype1 | 140 | 29 | 49 | 19 |
subtype2 | 66 | 13 | 31 | 23 |
subtype3 | 54 | 15 | 47 | 38 |
P value = 8e-05 (Fisher's exact test), Q value = 0.00037
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 265 | 69 | 179 | 11 |
subtype1 | 140 | 34 | 62 | 1 |
subtype2 | 67 | 16 | 44 | 6 |
subtype3 | 58 | 19 | 73 | 4 |
P value = 0.0108 (Fisher's exact test), Q value = 0.03
nPatients | 0 | 1 |
---|---|---|
ALL | 232 | 18 |
subtype1 | 108 | 3 |
subtype2 | 58 | 4 |
subtype3 | 66 | 11 |
P value = 6e-05 (Fisher's exact test), Q value = 0.00029
nPatients | 0 | 1 |
---|---|---|
ALL | 418 | 78 |
subtype1 | 203 | 19 |
subtype2 | 105 | 21 |
subtype3 | 110 | 38 |
P value = 0.0065 (Fisher's exact test), Q value = 0.019
nPatients | FEMALE | MALE |
---|---|---|
ALL | 188 | 336 |
subtype1 | 92 | 145 |
subtype2 | 56 | 77 |
subtype3 | 40 | 114 |
P value = 0.278 (Kruskal-Wallis (anova)), Q value = 0.4
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 44 | 88.2 (21.4) |
subtype1 | 18 | 92.8 (8.3) |
subtype2 | 8 | 95.0 (7.6) |
subtype3 | 18 | 80.6 (31.0) |
P value = 0.475 (Kruskal-Wallis (anova)), Q value = 0.63
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 15 | 28.9 (18.1) |
subtype1 | 7 | 33.0 (20.2) |
subtype2 | 3 | 33.3 (20.8) |
subtype3 | 5 | 20.6 (13.7) |
P value = 0.86 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 8 | 1979.6 (20.8) |
subtype1 | 4 | 1970.2 (22.8) |
subtype2 | 1 | 1996.0 (NA) |
subtype3 | 3 | 1986.7 (18.8) |
P value = 0.017 (Fisher's exact test), Q value = 0.043
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 8 | 52 | 457 |
subtype1 | 2 | 20 | 212 |
subtype2 | 4 | 22 | 106 |
subtype3 | 2 | 10 | 139 |
P value = 0.788 (Fisher's exact test), Q value = 0.97
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 26 | 345 |
subtype1 | 13 | 149 |
subtype2 | 7 | 95 |
subtype3 | 6 | 101 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 128 | 77 | 110 |
P value = 4.23e-06 (logrank test), Q value = 6.5e-05
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 313 | 100 | 0.1 - 120.6 (29.1) |
subtype1 | 127 | 21 | 0.1 - 120.6 (35.6) |
subtype2 | 76 | 25 | 0.5 - 109.9 (28.4) |
subtype3 | 110 | 54 | 0.2 - 90.1 (27.2) |
P value = 0.0178 (Kruskal-Wallis (anova)), Q value = 0.043
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 315 | 61.5 (11.8) |
subtype1 | 128 | 59.4 (12.7) |
subtype2 | 77 | 62.1 (11.4) |
subtype3 | 110 | 63.5 (10.7) |
P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 153 | 31 | 75 | 56 |
subtype1 | 87 | 17 | 14 | 10 |
subtype2 | 43 | 2 | 20 | 12 |
subtype3 | 23 | 12 | 41 | 34 |
P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 156 | 41 | 110 | 8 |
subtype1 | 87 | 21 | 20 | 0 |
subtype2 | 45 | 3 | 25 | 4 |
subtype3 | 24 | 17 | 65 | 4 |
P value = 0.25 (Fisher's exact test), Q value = 0.37
nPatients | 0 | 1 |
---|---|---|
ALL | 131 | 9 |
subtype1 | 52 | 1 |
subtype2 | 31 | 3 |
subtype3 | 48 | 5 |
P value = 0.00014 (Fisher's exact test), Q value = 0.00061
nPatients | 0 | 1 |
---|---|---|
ALL | 234 | 53 |
subtype1 | 103 | 10 |
subtype2 | 58 | 10 |
subtype3 | 73 | 33 |
P value = 2e-05 (Fisher's exact test), Q value = 0.00013
nPatients | FEMALE | MALE |
---|---|---|
ALL | 113 | 202 |
subtype1 | 61 | 67 |
subtype2 | 31 | 46 |
subtype3 | 21 | 89 |
P value = 0.343 (Kruskal-Wallis (anova)), Q value = 0.47
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 91.4 (9.3) |
subtype1 | 20 | 90.5 (10.5) |
subtype2 | 8 | 95.0 (7.6) |
subtype3 | 8 | 90.0 (7.6) |
P value = 0.762 (Kruskal-Wallis (anova)), Q value = 0.95
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 15 | 28.9 (18.1) |
subtype1 | 5 | 32.0 (24.0) |
subtype2 | 6 | 31.2 (18.0) |
subtype3 | 4 | 21.8 (11.4) |
P value = 0.663 (Kruskal-Wallis (anova)), Q value = 0.84
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 8 | 1979.6 (20.8) |
subtype1 | 3 | 1971.0 (27.8) |
subtype2 | 2 | 1980.5 (21.9) |
subtype3 | 3 | 1987.7 (17.1) |
P value = 0.0347 (Fisher's exact test), Q value = 0.077
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 1 | 45 | 266 |
subtype1 | 0 | 19 | 109 |
subtype2 | 0 | 17 | 60 |
subtype3 | 1 | 9 | 97 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 10 | 255 |
subtype1 | 4 | 98 |
subtype2 | 2 | 63 |
subtype3 | 4 | 94 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 108 | 62 | 77 | 81 | 81 | 45 |
P value = 1.65e-11 (logrank test), Q value = 1.2e-09
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 454 | 158 | 0.1 - 120.6 (37.1) |
subtype1 | 108 | 28 | 0.2 - 120.6 (46.5) |
subtype2 | 62 | 43 | 0.5 - 102.5 (22.7) |
subtype3 | 77 | 24 | 0.2 - 112.8 (36.4) |
subtype4 | 81 | 27 | 0.5 - 99.8 (37.2) |
subtype5 | 81 | 31 | 0.1 - 105.9 (40.7) |
subtype6 | 45 | 5 | 0.9 - 103.4 (37.0) |
P value = 0.173 (Kruskal-Wallis (anova)), Q value = 0.27
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 60.4 (12.3) |
subtype1 | 107 | 61.8 (10.9) |
subtype2 | 62 | 62.1 (11.9) |
subtype3 | 77 | 61.6 (12.4) |
subtype4 | 81 | 60.2 (11.7) |
subtype5 | 81 | 57.7 (12.3) |
subtype6 | 45 | 58.0 (16.0) |
P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 219 | 44 | 115 | 76 |
subtype1 | 58 | 12 | 24 | 14 |
subtype2 | 8 | 4 | 26 | 24 |
subtype3 | 33 | 10 | 23 | 11 |
subtype4 | 47 | 7 | 18 | 9 |
subtype5 | 38 | 9 | 16 | 18 |
subtype6 | 35 | 2 | 8 | 0 |
P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 224 | 54 | 165 | 11 |
subtype1 | 58 | 16 | 33 | 1 |
subtype2 | 9 | 9 | 40 | 4 |
subtype3 | 35 | 10 | 32 | 0 |
subtype4 | 48 | 7 | 25 | 1 |
subtype5 | 39 | 10 | 27 | 5 |
subtype6 | 35 | 2 | 8 | 0 |
P value = 0.0121 (Fisher's exact test), Q value = 0.032
nPatients | 0 | 1 |
---|---|---|
ALL | 208 | 16 |
subtype1 | 51 | 1 |
subtype2 | 26 | 8 |
subtype3 | 40 | 2 |
subtype4 | 38 | 3 |
subtype5 | 39 | 2 |
subtype6 | 14 | 0 |
P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05
nPatients | 0 | 1 |
---|---|---|
ALL | 379 | 75 |
subtype1 | 94 | 14 |
subtype2 | 38 | 24 |
subtype3 | 66 | 11 |
subtype4 | 72 | 9 |
subtype5 | 64 | 17 |
subtype6 | 45 | 0 |
P value = 0.102 (Fisher's exact test), Q value = 0.19
nPatients | FEMALE | MALE |
---|---|---|
ALL | 151 | 303 |
subtype1 | 46 | 62 |
subtype2 | 16 | 46 |
subtype3 | 23 | 54 |
subtype4 | 22 | 59 |
subtype5 | 25 | 56 |
subtype6 | 19 | 26 |
P value = 0.109 (Kruskal-Wallis (anova)), Q value = 0.2
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 34 | 93.5 (7.7) |
subtype1 | 7 | 91.4 (6.9) |
subtype2 | 3 | 93.3 (11.5) |
subtype3 | 10 | 90.0 (9.4) |
subtype4 | 3 | 100.0 (0.0) |
subtype5 | 7 | 94.3 (5.3) |
subtype6 | 4 | 100.0 (0.0) |
P value = 0.112 (Fisher's exact test), Q value = 0.2
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 8 | 20 | 420 |
subtype1 | 0 | 5 | 101 |
subtype2 | 2 | 0 | 60 |
subtype3 | 1 | 1 | 71 |
subtype4 | 1 | 7 | 73 |
subtype5 | 3 | 5 | 73 |
subtype6 | 1 | 2 | 42 |
P value = 0.351 (Fisher's exact test), Q value = 0.48
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 19 | 295 |
subtype1 | 6 | 72 |
subtype2 | 3 | 45 |
subtype3 | 5 | 53 |
subtype4 | 1 | 45 |
subtype5 | 1 | 55 |
subtype6 | 3 | 25 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 122 | 200 | 132 |
P value = 1.32e-13 (logrank test), Q value = 1.9e-11
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 454 | 158 | 0.1 - 120.6 (37.1) |
subtype1 | 122 | 32 | 0.4 - 120.6 (44.3) |
subtype2 | 200 | 47 | 0.5 - 105.9 (38.8) |
subtype3 | 132 | 79 | 0.1 - 112.8 (27.1) |
P value = 0.111 (Kruskal-Wallis (anova)), Q value = 0.2
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 60.4 (12.3) |
subtype1 | 121 | 60.9 (12.0) |
subtype2 | 200 | 59.0 (13.0) |
subtype3 | 132 | 62.0 (11.2) |
P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 219 | 44 | 115 | 76 |
subtype1 | 54 | 15 | 39 | 14 |
subtype2 | 130 | 16 | 37 | 17 |
subtype3 | 35 | 13 | 39 | 45 |
P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 224 | 54 | 165 | 11 |
subtype1 | 55 | 17 | 49 | 1 |
subtype2 | 132 | 19 | 48 | 1 |
subtype3 | 37 | 18 | 68 | 9 |
P value = 0.0527 (Fisher's exact test), Q value = 0.11
nPatients | 0 | 1 |
---|---|---|
ALL | 208 | 16 |
subtype1 | 63 | 2 |
subtype2 | 78 | 4 |
subtype3 | 67 | 10 |
P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05
nPatients | 0 | 1 |
---|---|---|
ALL | 379 | 75 |
subtype1 | 109 | 13 |
subtype2 | 182 | 18 |
subtype3 | 88 | 44 |
P value = 0.105 (Fisher's exact test), Q value = 0.19
nPatients | FEMALE | MALE |
---|---|---|
ALL | 151 | 303 |
subtype1 | 34 | 88 |
subtype2 | 77 | 123 |
subtype3 | 40 | 92 |
P value = 0.0648 (Kruskal-Wallis (anova)), Q value = 0.14
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 34 | 93.5 (7.7) |
subtype1 | 8 | 90.0 (9.3) |
subtype2 | 16 | 96.9 (4.8) |
subtype3 | 10 | 91.0 (8.8) |
P value = 0.85 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 8 | 20 | 420 |
subtype1 | 1 | 4 | 115 |
subtype2 | 4 | 9 | 184 |
subtype3 | 3 | 7 | 121 |
P value = 0.0686 (Fisher's exact test), Q value = 0.14
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 19 | 295 |
subtype1 | 9 | 82 |
subtype2 | 8 | 117 |
subtype3 | 2 | 96 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 114 | 222 | 193 |
P value = 7.09e-07 (logrank test), Q value = 2.6e-05
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 527 | 168 | 0.1 - 120.6 (36.4) |
subtype1 | 113 | 32 | 0.1 - 112.8 (37.6) |
subtype2 | 221 | 48 | 0.1 - 120.6 (37.4) |
subtype3 | 193 | 88 | 0.2 - 109.9 (30.5) |
P value = 0.143 (Kruskal-Wallis (anova)), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 528 | 60.7 (12.2) |
subtype1 | 114 | 58.6 (12.7) |
subtype2 | 221 | 61.5 (12.1) |
subtype3 | 193 | 60.9 (11.7) |
P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 265 | 57 | 126 | 81 |
subtype1 | 70 | 12 | 20 | 12 |
subtype2 | 134 | 23 | 41 | 24 |
subtype3 | 61 | 22 | 65 | 45 |
P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 270 | 69 | 179 | 11 |
subtype1 | 70 | 13 | 28 | 3 |
subtype2 | 134 | 27 | 59 | 2 |
subtype3 | 66 | 29 | 92 | 6 |
P value = 0.0127 (Fisher's exact test), Q value = 0.033
nPatients | 0 | 1 |
---|---|---|
ALL | 238 | 17 |
subtype1 | 50 | 3 |
subtype2 | 100 | 2 |
subtype3 | 88 | 12 |
P value = 0.00039 (Fisher's exact test), Q value = 0.0016
nPatients | 0 | 1 |
---|---|---|
ALL | 422 | 79 |
subtype1 | 96 | 11 |
subtype2 | 185 | 23 |
subtype3 | 141 | 45 |
P value = 5e-05 (Fisher's exact test), Q value = 0.00025
nPatients | FEMALE | MALE |
---|---|---|
ALL | 187 | 342 |
subtype1 | 39 | 75 |
subtype2 | 101 | 121 |
subtype3 | 47 | 146 |
P value = 0.315 (Kruskal-Wallis (anova)), Q value = 0.45
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 43 | 90.2 (16.7) |
subtype1 | 9 | 95.6 (7.3) |
subtype2 | 19 | 90.0 (10.5) |
subtype3 | 15 | 87.3 (25.2) |
P value = 0.807 (Kruskal-Wallis (anova)), Q value = 0.98
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 15 | 28.9 (18.1) |
subtype1 | 4 | 26.0 (18.2) |
subtype2 | 5 | 34.0 (24.2) |
subtype3 | 6 | 26.7 (14.6) |
P value = 0.858 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 8 | 1979.6 (20.8) |
subtype1 | 1 | 1999.0 (NA) |
subtype2 | 3 | 1971.0 (27.8) |
subtype3 | 4 | 1981.2 (17.1) |
P value = 0.0195 (Fisher's exact test), Q value = 0.047
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 8 | 52 | 462 |
subtype1 | 4 | 19 | 90 |
subtype2 | 2 | 19 | 197 |
subtype3 | 2 | 14 | 175 |
P value = 0.107 (Fisher's exact test), Q value = 0.19
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 26 | 350 |
subtype1 | 3 | 80 |
subtype2 | 16 | 140 |
subtype3 | 7 | 130 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 118 | 34 | 183 | 132 | 35 | 27 |
P value = 3.67e-08 (logrank test), Q value = 1.8e-06
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 527 | 168 | 0.1 - 120.6 (36.4) |
subtype1 | 118 | 32 | 0.1 - 97.4 (30.3) |
subtype2 | 33 | 6 | 0.5 - 112.8 (37.1) |
subtype3 | 182 | 38 | 0.1 - 120.6 (42.3) |
subtype4 | 132 | 71 | 0.2 - 109.9 (31.5) |
subtype5 | 35 | 15 | 0.1 - 102.5 (36.4) |
subtype6 | 27 | 6 | 3.6 - 84.4 (43.2) |
P value = 0.119 (Kruskal-Wallis (anova)), Q value = 0.2
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 528 | 60.7 (12.2) |
subtype1 | 118 | 58.8 (12.3) |
subtype2 | 34 | 57.8 (13.8) |
subtype3 | 182 | 61.5 (12.2) |
subtype4 | 132 | 62.4 (11.4) |
subtype5 | 35 | 58.3 (11.9) |
subtype6 | 27 | 61.4 (11.5) |
P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 265 | 57 | 126 | 81 |
subtype1 | 62 | 12 | 24 | 20 |
subtype2 | 25 | 4 | 2 | 3 |
subtype3 | 116 | 19 | 36 | 12 |
subtype4 | 37 | 13 | 47 | 35 |
subtype5 | 5 | 5 | 15 | 10 |
subtype6 | 20 | 4 | 2 | 1 |
P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 270 | 69 | 179 | 11 |
subtype1 | 63 | 17 | 36 | 2 |
subtype2 | 25 | 4 | 5 | 0 |
subtype3 | 116 | 21 | 46 | 0 |
subtype4 | 39 | 15 | 71 | 7 |
subtype5 | 7 | 8 | 19 | 1 |
subtype6 | 20 | 4 | 2 | 1 |
P value = 0.00399 (Fisher's exact test), Q value = 0.013
nPatients | 0 | 1 |
---|---|---|
ALL | 238 | 17 |
subtype1 | 43 | 1 |
subtype2 | 15 | 1 |
subtype3 | 84 | 1 |
subtype4 | 66 | 10 |
subtype5 | 17 | 4 |
subtype6 | 13 | 0 |
P value = 5e-05 (Fisher's exact test), Q value = 0.00025
nPatients | 0 | 1 |
---|---|---|
ALL | 422 | 79 |
subtype1 | 94 | 18 |
subtype2 | 28 | 3 |
subtype3 | 158 | 13 |
subtype4 | 95 | 34 |
subtype5 | 22 | 10 |
subtype6 | 25 | 1 |
P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05
nPatients | FEMALE | MALE |
---|---|---|
ALL | 187 | 342 |
subtype1 | 16 | 102 |
subtype2 | 16 | 18 |
subtype3 | 101 | 82 |
subtype4 | 31 | 101 |
subtype5 | 17 | 18 |
subtype6 | 6 | 21 |
P value = 0.278 (Kruskal-Wallis (anova)), Q value = 0.4
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 43 | 90.2 (16.7) |
subtype1 | 8 | 95.0 (5.3) |
subtype2 | 6 | 95.0 (12.2) |
subtype3 | 16 | 90.6 (10.0) |
subtype4 | 9 | 81.1 (31.4) |
subtype5 | 1 | 80.0 (NA) |
subtype6 | 3 | 96.7 (5.8) |
P value = 0.685 (Kruskal-Wallis (anova)), Q value = 0.86
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 15 | 28.9 (18.1) |
subtype1 | 4 | 30.8 (13.1) |
subtype2 | 2 | 45.0 (7.1) |
subtype3 | 4 | 31.0 (26.8) |
subtype4 | 3 | 20.0 (17.3) |
subtype5 | 2 | 18.5 (16.3) |
P value = 0.00226 (Fisher's exact test), Q value = 0.0076
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 8 | 52 | 462 |
subtype1 | 3 | 11 | 100 |
subtype2 | 2 | 9 | 23 |
subtype3 | 1 | 16 | 164 |
subtype4 | 2 | 6 | 124 |
subtype5 | 0 | 4 | 30 |
subtype6 | 0 | 6 | 21 |
P value = 0.656 (Fisher's exact test), Q value = 0.84
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 26 | 350 |
subtype1 | 6 | 74 |
subtype2 | 2 | 29 |
subtype3 | 12 | 110 |
subtype4 | 5 | 88 |
subtype5 | 1 | 26 |
subtype6 | 0 | 23 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 125 | 204 | 183 |
P value = 8.12e-06 (logrank test), Q value = 6.5e-05
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 510 | 166 | 0.1 - 120.6 (36.3) |
subtype1 | 124 | 32 | 0.1 - 112.8 (41.2) |
subtype2 | 203 | 49 | 0.2 - 120.6 (36.9) |
subtype3 | 183 | 85 | 0.2 - 94.0 (31.9) |
P value = 0.0383 (Kruskal-Wallis (anova)), Q value = 0.084
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 512 | 60.6 (12.1) |
subtype1 | 125 | 58.5 (12.1) |
subtype2 | 204 | 62.2 (12.3) |
subtype3 | 183 | 60.3 (11.6) |
P value = 0.00023 (Fisher's exact test), Q value = 0.00095
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 251 | 55 | 126 | 80 |
subtype1 | 76 | 11 | 28 | 10 |
subtype2 | 110 | 20 | 46 | 28 |
subtype3 | 65 | 24 | 52 | 42 |
P value = 5e-04 (Fisher's exact test), Q value = 0.0019
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 256 | 67 | 178 | 11 |
subtype1 | 77 | 11 | 33 | 4 |
subtype2 | 111 | 26 | 65 | 2 |
subtype3 | 68 | 30 | 80 | 5 |
P value = 0.0114 (Fisher's exact test), Q value = 0.03
nPatients | 0 | 1 |
---|---|---|
ALL | 226 | 18 |
subtype1 | 56 | 3 |
subtype2 | 87 | 2 |
subtype3 | 83 | 13 |
P value = 0.00073 (Fisher's exact test), Q value = 0.0027
nPatients | 0 | 1 |
---|---|---|
ALL | 406 | 78 |
subtype1 | 105 | 9 |
subtype2 | 168 | 27 |
subtype3 | 133 | 42 |
P value = 0.00226 (Fisher's exact test), Q value = 0.0076
nPatients | FEMALE | MALE |
---|---|---|
ALL | 180 | 332 |
subtype1 | 44 | 81 |
subtype2 | 88 | 116 |
subtype3 | 48 | 135 |
P value = 0.908 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 44 | 88.2 (21.4) |
subtype1 | 14 | 91.4 (11.7) |
subtype2 | 19 | 92.1 (7.9) |
subtype3 | 11 | 77.3 (38.8) |
P value = 0.322 (Kruskal-Wallis (anova)), Q value = 0.45
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 15 | 28.9 (18.1) |
subtype1 | 5 | 21.2 (14.3) |
subtype2 | 4 | 40.2 (22.8) |
subtype3 | 6 | 27.8 (16.7) |
P value = 1 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 8 | 1979.6 (20.8) |
subtype1 | 3 | 1977.3 (18.8) |
subtype2 | 3 | 1971.0 (27.8) |
subtype3 | 2 | 1996.0 (0.0) |
P value = 0.208 (Fisher's exact test), Q value = 0.32
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 8 | 52 | 445 |
subtype1 | 1 | 19 | 104 |
subtype2 | 3 | 15 | 182 |
subtype3 | 4 | 18 | 159 |
P value = 0.181 (Fisher's exact test), Q value = 0.28
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 24 | 340 |
subtype1 | 2 | 82 |
subtype2 | 12 | 132 |
subtype3 | 10 | 126 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 144 | 136 | 195 | 37 |
P value = 0.000219 (logrank test), Q value = 0.00093
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 510 | 166 | 0.1 - 120.6 (36.3) |
subtype1 | 143 | 49 | 0.1 - 112.8 (33.5) |
subtype2 | 136 | 49 | 0.1 - 94.0 (32.2) |
subtype3 | 194 | 44 | 0.1 - 120.6 (38.1) |
subtype4 | 37 | 24 | 1.4 - 89.4 (44.0) |
P value = 0.0794 (Kruskal-Wallis (anova)), Q value = 0.16
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 512 | 60.6 (12.1) |
subtype1 | 144 | 59.2 (12.4) |
subtype2 | 136 | 59.6 (11.9) |
subtype3 | 195 | 61.7 (12.0) |
subtype4 | 37 | 64.2 (11.0) |
P value = 5e-05 (Fisher's exact test), Q value = 0.00025
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 251 | 55 | 126 | 80 |
subtype1 | 81 | 10 | 36 | 17 |
subtype2 | 51 | 17 | 35 | 33 |
subtype3 | 110 | 24 | 43 | 18 |
subtype4 | 9 | 4 | 12 | 12 |
P value = 9e-05 (Fisher's exact test), Q value = 4e-04
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 256 | 67 | 178 | 11 |
subtype1 | 82 | 11 | 46 | 5 |
subtype2 | 53 | 23 | 57 | 3 |
subtype3 | 112 | 28 | 54 | 1 |
subtype4 | 9 | 5 | 21 | 2 |
P value = 0.0202 (Fisher's exact test), Q value = 0.048
nPatients | 0 | 1 |
---|---|---|
ALL | 226 | 18 |
subtype1 | 61 | 8 |
subtype2 | 65 | 8 |
subtype3 | 84 | 1 |
subtype4 | 16 | 1 |
P value = 5e-05 (Fisher's exact test), Q value = 0.00025
nPatients | 0 | 1 |
---|---|---|
ALL | 406 | 78 |
subtype1 | 119 | 15 |
subtype2 | 98 | 32 |
subtype3 | 165 | 18 |
subtype4 | 24 | 13 |
P value = 0.00114 (Fisher's exact test), Q value = 0.004
nPatients | FEMALE | MALE |
---|---|---|
ALL | 180 | 332 |
subtype1 | 54 | 90 |
subtype2 | 36 | 100 |
subtype3 | 84 | 111 |
subtype4 | 6 | 31 |
P value = 0.166 (Kruskal-Wallis (anova)), Q value = 0.27
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 44 | 88.2 (21.4) |
subtype1 | 15 | 88.7 (25.3) |
subtype2 | 11 | 80.0 (28.3) |
subtype3 | 17 | 92.4 (9.7) |
subtype4 | 1 | 100.0 (NA) |
P value = 0.807 (Kruskal-Wallis (anova)), Q value = 0.98
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 15 | 28.9 (18.1) |
subtype1 | 4 | 23.5 (14.0) |
subtype2 | 6 | 28.3 (16.9) |
subtype3 | 5 | 34.0 (24.2) |
P value = 0.658 (Kruskal-Wallis (anova)), Q value = 0.84
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 8 | 1979.6 (20.8) |
subtype1 | 2 | 1982.0 (24.0) |
subtype2 | 3 | 1986.7 (16.2) |
subtype3 | 3 | 1971.0 (27.8) |
P value = 0.13 (Fisher's exact test), Q value = 0.22
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 8 | 52 | 445 |
subtype1 | 4 | 20 | 120 |
subtype2 | 2 | 14 | 117 |
subtype3 | 2 | 18 | 171 |
subtype4 | 0 | 0 | 37 |
P value = 0.0175 (Fisher's exact test), Q value = 0.043
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 24 | 340 |
subtype1 | 2 | 93 |
subtype2 | 4 | 98 |
subtype3 | 14 | 123 |
subtype4 | 4 | 26 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 36 | 22 | 49 | 35 |
P value = 0.00975 (logrank test), Q value = 0.028
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 140 | 42 | 0.1 - 120.6 (33.2) |
subtype1 | 34 | 8 | 0.1 - 77.4 (19.0) |
subtype2 | 22 | 4 | 6.9 - 112.8 (35.9) |
subtype3 | 49 | 12 | 0.8 - 120.6 (38.7) |
subtype4 | 35 | 18 | 0.5 - 87.5 (30.6) |
P value = 0.706 (Kruskal-Wallis (anova)), Q value = 0.88
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 142 | 60.7 (11.6) |
subtype1 | 36 | 60.7 (10.9) |
subtype2 | 22 | 58.0 (12.0) |
subtype3 | 49 | 61.7 (12.3) |
subtype4 | 35 | 61.2 (11.3) |
P value = 0.305 (Fisher's exact test), Q value = 0.44
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 73 | 17 | 26 | 26 |
subtype1 | 22 | 5 | 4 | 5 |
subtype2 | 15 | 1 | 4 | 2 |
subtype3 | 22 | 7 | 12 | 8 |
subtype4 | 14 | 4 | 6 | 11 |
P value = 0.102 (Fisher's exact test), Q value = 0.19
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 75 | 19 | 43 | 5 |
subtype1 | 22 | 6 | 7 | 1 |
subtype2 | 16 | 1 | 4 | 1 |
subtype3 | 22 | 8 | 19 | 0 |
subtype4 | 15 | 4 | 13 | 3 |
P value = 0.2 (Fisher's exact test), Q value = 0.31
nPatients | 0 | 1 |
---|---|---|
ALL | 56 | 5 |
subtype1 | 7 | 1 |
subtype2 | 9 | 1 |
subtype3 | 23 | 0 |
subtype4 | 17 | 3 |
P value = 0.116 (Fisher's exact test), Q value = 0.2
nPatients | 0 | 1 |
---|---|---|
ALL | 98 | 23 |
subtype1 | 14 | 4 |
subtype2 | 20 | 1 |
subtype3 | 41 | 8 |
subtype4 | 23 | 10 |
P value = 0.0331 (Fisher's exact test), Q value = 0.074
nPatients | FEMALE | MALE |
---|---|---|
ALL | 49 | 93 |
subtype1 | 17 | 19 |
subtype2 | 6 | 16 |
subtype3 | 20 | 29 |
subtype4 | 6 | 29 |
P value = 0.985 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 20 | 91.5 (10.9) |
subtype1 | 7 | 90.0 (14.1) |
subtype3 | 9 | 92.2 (9.7) |
subtype4 | 4 | 92.5 (9.6) |
P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 28 | 108 |
subtype1 | 0 | 22 | 14 |
subtype2 | 1 | 2 | 18 |
subtype3 | 0 | 0 | 48 |
subtype4 | 2 | 4 | 28 |
P value = 0.325 (Fisher's exact test), Q value = 0.45
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 6 | 101 |
subtype1 | 0 | 29 |
subtype2 | 1 | 13 |
subtype3 | 4 | 37 |
subtype4 | 1 | 22 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 38 | 56 | 48 |
P value = 0.577 (logrank test), Q value = 0.76
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 140 | 42 | 0.1 - 120.6 (33.2) |
subtype1 | 36 | 8 | 0.1 - 77.4 (17.9) |
subtype2 | 56 | 21 | 0.5 - 112.8 (35.9) |
subtype3 | 48 | 13 | 0.8 - 120.6 (36.5) |
P value = 0.0635 (Kruskal-Wallis (anova)), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 142 | 60.7 (11.6) |
subtype1 | 38 | 61.0 (10.7) |
subtype2 | 56 | 58.1 (11.7) |
subtype3 | 48 | 63.6 (11.8) |
P value = 0.24 (Fisher's exact test), Q value = 0.36
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 73 | 17 | 26 | 26 |
subtype1 | 25 | 4 | 4 | 5 |
subtype2 | 27 | 4 | 12 | 13 |
subtype3 | 21 | 9 | 10 | 8 |
P value = 0.0285 (Fisher's exact test), Q value = 0.065
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 75 | 19 | 43 | 5 |
subtype1 | 26 | 5 | 6 | 1 |
subtype2 | 27 | 4 | 21 | 4 |
subtype3 | 22 | 10 | 16 | 0 |
P value = 0.169 (Fisher's exact test), Q value = 0.27
nPatients | 0 | 1 |
---|---|---|
ALL | 56 | 5 |
subtype1 | 8 | 1 |
subtype2 | 26 | 4 |
subtype3 | 22 | 0 |
P value = 0.866 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 98 | 23 |
subtype1 | 17 | 4 |
subtype2 | 41 | 11 |
subtype3 | 40 | 8 |
P value = 0.00292 (Fisher's exact test), Q value = 0.0096
nPatients | FEMALE | MALE |
---|---|---|
ALL | 49 | 93 |
subtype1 | 17 | 21 |
subtype2 | 10 | 46 |
subtype3 | 22 | 26 |
P value = 0.848 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 20 | 91.5 (10.9) |
subtype1 | 7 | 90.0 (14.1) |
subtype2 | 5 | 94.0 (8.9) |
subtype3 | 8 | 91.2 (9.9) |
P value = 1 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 8 | 27.2 (20.2) |
subtype1 | 4 | 28.5 (26.2) |
subtype2 | 3 | 21.3 (16.3) |
subtype3 | 1 | 40.0 (NA) |
P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 28 | 108 |
subtype1 | 0 | 21 | 17 |
subtype2 | 3 | 6 | 46 |
subtype3 | 0 | 1 | 45 |
P value = 0.276 (Fisher's exact test), Q value = 0.4
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 6 | 101 |
subtype1 | 0 | 31 |
subtype2 | 3 | 35 |
subtype3 | 3 | 35 |
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Cluster data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRC-TP/15107132/KIRC-TP.mergedcluster.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIRC-TP/15081616/KIRC-TP.merged_data.txt
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Number of patients = 533
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Number of clustering approaches = 12
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Number of selected clinical features = 12
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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 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 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.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.