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 92 patients, 26 significant findings detected with P value < 0.05 and Q value < 0.25.
-
4 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes correlate to 'Time to Death', 'YEARS_TO_BIRTH', and 'PATHOLOGY_N_STAGE'.
-
5 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'Time to Death' and 'GENDER'.
-
CNMF clustering analysis on RPPA data identified 2 subtypes that correlate to 'Time to Death'.
-
Consensus hierarchical clustering analysis on RPPA data identified 8 subtypes that correlate to 'Time to Death'.
-
CNMF clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that correlate to 'Time to Death', 'NEOPLASM_DISEASESTAGE', and 'PATHOLOGY_N_STAGE'.
-
Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that correlate to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'RACE'.
-
3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', and 'PATHOLOGY_N_STAGE'.
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5 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes correlate to 'Time to Death' and 'NEOPLASM_DISEASESTAGE'.
-
3 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes correlate to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', and 'PATHOLOGY_N_STAGE'.
-
3 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes correlate to 'NEOPLASM_DISEASESTAGE'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
GENDER | 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 | Fisher's exact test |
Copy Number Ratio CNMF subtypes |
0.00392 (0.0285) |
0.0265 (0.111) |
0.225 (0.408) |
0.746 (0.866) |
0.00575 (0.0313) |
0.732 (0.866) |
0.819 (0.923) |
0.22 (0.408) |
METHLYATION CNMF |
0.000355 (0.00651) |
0.323 (0.497) |
0.231 (0.408) |
0.172 (0.344) |
0.0991 (0.24) |
0.0005 (0.00651) |
0.548 (0.708) |
0.749 (0.866) |
RPPA CNMF subtypes |
0.0331 (0.125) |
0.676 (0.832) |
0.0825 (0.22) |
0.123 (0.281) |
0.667 (0.832) |
1 (1.00) |
0.203 (0.397) |
1 (1.00) |
RPPA cHierClus subtypes |
0.0429 (0.143) |
0.491 (0.644) |
0.0713 (0.197) |
0.136 (0.298) |
0.469 (0.626) |
0.468 (0.626) |
0.264 (0.424) |
0.758 (0.866) |
RNAseq CNMF subtypes |
0.000309 (0.00651) |
0.906 (0.992) |
0.013 (0.0614) |
0.0973 (0.24) |
0.0483 (0.148) |
0.239 (0.408) |
0.303 (0.475) |
0.944 (1.00) |
RNAseq cHierClus subtypes |
0.000278 (0.00651) |
0.623 (0.791) |
0.00442 (0.0295) |
0.0359 (0.125) |
0.0357 (0.125) |
0.359 (0.528) |
0.00924 (0.0462) |
0.24 (0.408) |
MIRSEQ CNMF |
0.00588 (0.0313) |
0.219 (0.408) |
0.00051 (0.00651) |
0.00531 (0.0313) |
0.0457 (0.146) |
0.138 (0.298) |
1 (1.00) |
0.385 (0.55) |
MIRSEQ CHIERARCHICAL |
0.0277 (0.111) |
0.265 (0.424) |
0.0009 (0.00809) |
0.153 (0.319) |
0.254 (0.423) |
0.33 (0.499) |
0.105 (0.247) |
0.699 (0.847) |
MIRseq Mature CNMF subtypes |
0.000208 (0.00651) |
0.412 (0.568) |
0.00057 (0.00651) |
0.00091 (0.00809) |
0.0276 (0.111) |
0.0611 (0.181) |
1 (1.00) |
0.866 (0.963) |
MIRseq Mature cHierClus subtypes |
0.0634 (0.181) |
0.969 (1.00) |
0.00317 (0.0254) |
0.0907 (0.234) |
0.155 (0.319) |
0.363 (0.528) |
0.408 (0.568) |
1 (1.00) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 36 | 26 | 16 | 12 |
P value = 0.00392 (logrank test), Q value = 0.029
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 90 | 32 | 0.0 - 153.6 (36.3) |
subtype1 | 36 | 18 | 0.0 - 152.2 (33.3) |
subtype2 | 26 | 3 | 5.2 - 153.6 (31.5) |
subtype3 | 16 | 9 | 12.0 - 69.1 (36.2) |
subtype4 | 12 | 2 | 4.1 - 91.5 (54.9) |
P value = 0.0265 (Kruskal-Wallis (anova)), Q value = 0.11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 90 | 47.1 (16.5) |
subtype1 | 36 | 48.5 (17.9) |
subtype2 | 26 | 53.1 (14.3) |
subtype3 | 16 | 39.2 (15.1) |
subtype4 | 12 | 40.6 (12.8) |
P value = 0.225 (Fisher's exact test), Q value = 0.41
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 9 | 43 | 18 | 18 |
subtype1 | 5 | 15 | 8 | 7 |
subtype2 | 2 | 15 | 6 | 3 |
subtype3 | 0 | 5 | 3 | 7 |
subtype4 | 2 | 8 | 1 | 1 |
P value = 0.746 (Fisher's exact test), Q value = 0.87
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 9 | 48 | 11 | 20 |
subtype1 | 5 | 16 | 5 | 9 |
subtype2 | 2 | 16 | 3 | 5 |
subtype3 | 0 | 8 | 2 | 5 |
subtype4 | 2 | 8 | 1 | 1 |
P value = 0.00575 (Fisher's exact test), Q value = 0.031
nPatients | 0 | 1 |
---|---|---|
ALL | 78 | 10 |
subtype1 | 33 | 2 |
subtype2 | 24 | 2 |
subtype3 | 9 | 6 |
subtype4 | 12 | 0 |
P value = 0.732 (Fisher's exact test), Q value = 0.87
nPatients | FEMALE | MALE |
---|---|---|
ALL | 59 | 31 |
subtype1 | 26 | 10 |
subtype2 | 16 | 10 |
subtype3 | 10 | 6 |
subtype4 | 7 | 5 |
P value = 0.819 (Fisher's exact test), Q value = 0.92
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 2 | 1 | 76 |
subtype1 | 2 | 1 | 30 |
subtype2 | 0 | 0 | 24 |
subtype3 | 0 | 0 | 13 |
subtype4 | 0 | 0 | 9 |
P value = 0.22 (Fisher's exact test), Q value = 0.41
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 38 |
subtype1 | 3 | 16 |
subtype2 | 1 | 13 |
subtype3 | 4 | 6 |
subtype4 | 0 | 3 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 18 | 11 | 22 | 18 | 11 |
P value = 0.000355 (logrank test), Q value = 0.0065
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 80 | 28 | 4.1 - 153.6 (36.3) |
subtype1 | 18 | 13 | 4.1 - 127.5 (20.1) |
subtype2 | 11 | 3 | 18.1 - 152.2 (52.2) |
subtype3 | 22 | 8 | 6.8 - 153.6 (39.0) |
subtype4 | 18 | 3 | 12.6 - 121.2 (29.5) |
subtype5 | 11 | 1 | 12.6 - 91.5 (36.3) |
P value = 0.323 (Kruskal-Wallis (anova)), Q value = 0.5
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 46.4 (15.9) |
subtype1 | 18 | 40.3 (20.0) |
subtype2 | 11 | 53.2 (14.8) |
subtype3 | 22 | 46.8 (14.2) |
subtype4 | 18 | 49.4 (12.4) |
subtype5 | 11 | 43.9 (16.4) |
P value = 0.231 (Fisher's exact test), Q value = 0.41
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 9 | 37 | 16 | 16 |
subtype1 | 1 | 7 | 6 | 4 |
subtype2 | 1 | 3 | 4 | 3 |
subtype3 | 2 | 9 | 3 | 6 |
subtype4 | 3 | 9 | 3 | 3 |
subtype5 | 2 | 9 | 0 | 0 |
P value = 0.172 (Fisher's exact test), Q value = 0.34
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 9 | 42 | 9 | 18 |
subtype1 | 1 | 9 | 3 | 5 |
subtype2 | 1 | 5 | 4 | 1 |
subtype3 | 2 | 10 | 1 | 7 |
subtype4 | 3 | 9 | 1 | 5 |
subtype5 | 2 | 9 | 0 | 0 |
P value = 0.0991 (Fisher's exact test), Q value = 0.24
nPatients | 0 | 1 |
---|---|---|
ALL | 68 | 10 |
subtype1 | 14 | 4 |
subtype2 | 9 | 2 |
subtype3 | 16 | 4 |
subtype4 | 18 | 0 |
subtype5 | 11 | 0 |
P value = 5e-04 (Fisher's exact test), Q value = 0.0065
nPatients | FEMALE | MALE |
---|---|---|
ALL | 49 | 31 |
subtype1 | 13 | 5 |
subtype2 | 9 | 2 |
subtype3 | 7 | 15 |
subtype4 | 9 | 9 |
subtype5 | 11 | 0 |
P value = 0.548 (Fisher's exact test), Q value = 0.71
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 1 | 1 | 67 |
subtype1 | 0 | 0 | 18 |
subtype2 | 0 | 0 | 9 |
subtype3 | 0 | 0 | 17 |
subtype4 | 1 | 1 | 15 |
subtype5 | 0 | 0 | 8 |
P value = 0.749 (Fisher's exact test), Q value = 0.87
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 30 |
subtype1 | 3 | 6 |
subtype2 | 2 | 6 |
subtype3 | 1 | 8 |
subtype4 | 2 | 6 |
subtype5 | 0 | 4 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 22 | 24 |
P value = 0.0331 (logrank test), Q value = 0.12
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 46 | 13 | 4.1 - 153.6 (42.0) |
subtype1 | 22 | 4 | 12.6 - 153.6 (58.1) |
subtype2 | 24 | 9 | 4.1 - 72.4 (37.4) |
P value = 0.676 (Wilcoxon-test), Q value = 0.83
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 46 | 47.2 (14.4) |
subtype1 | 22 | 46.4 (13.5) |
subtype2 | 24 | 47.9 (15.5) |
P value = 0.0825 (Fisher's exact test), Q value = 0.22
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 2 | 26 | 10 | 8 |
subtype1 | 2 | 15 | 2 | 3 |
subtype2 | 0 | 11 | 8 | 5 |
P value = 0.123 (Fisher's exact test), Q value = 0.28
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 2 | 30 | 7 | 7 |
subtype1 | 2 | 16 | 1 | 3 |
subtype2 | 0 | 14 | 6 | 4 |
P value = 0.667 (Fisher's exact test), Q value = 0.83
nPatients | 0 | 1 |
---|---|---|
ALL | 40 | 6 |
subtype1 | 20 | 2 |
subtype2 | 20 | 4 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 28 | 18 |
subtype1 | 13 | 9 |
subtype2 | 15 | 9 |
P value = 0.203 (Fisher's exact test), Q value = 0.4
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 1 | 1 | 35 |
subtype1 | 1 | 1 | 15 |
subtype2 | 0 | 0 | 20 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 6 | 17 |
subtype1 | 2 | 7 |
subtype2 | 4 | 10 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 |
---|---|---|---|---|---|---|---|---|
Number of samples | 8 | 7 | 7 | 3 | 4 | 4 | 7 | 6 |
P value = 0.0429 (logrank test), Q value = 0.14
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 46 | 13 | 4.1 - 153.6 (42.0) |
subtype1 | 8 | 4 | 4.1 - 69.1 (37.8) |
subtype2 | 7 | 3 | 12.8 - 68.8 (30.3) |
subtype3 | 7 | 0 | 24.9 - 88.9 (39.5) |
subtype4 | 3 | 1 | 15.2 - 44.8 (16.1) |
subtype5 | 4 | 3 | 12.6 - 153.6 (18.6) |
subtype6 | 4 | 0 | 18.1 - 121.2 (79.8) |
subtype7 | 7 | 1 | 12.6 - 119.1 (66.5) |
subtype8 | 6 | 1 | 20.2 - 72.4 (50.7) |
P value = 0.491 (Kruskal-Wallis (anova)), Q value = 0.64
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 46 | 47.2 (14.4) |
subtype1 | 8 | 47.2 (15.0) |
subtype2 | 7 | 41.6 (14.8) |
subtype3 | 7 | 52.4 (14.2) |
subtype4 | 3 | 31.7 (7.6) |
subtype5 | 4 | 54.0 (15.4) |
subtype6 | 4 | 45.2 (10.8) |
subtype7 | 7 | 48.3 (15.4) |
subtype8 | 6 | 50.7 (15.6) |
P value = 0.0713 (Fisher's exact test), Q value = 0.2
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 2 | 26 | 10 | 8 |
subtype1 | 0 | 5 | 1 | 2 |
subtype2 | 0 | 1 | 3 | 3 |
subtype3 | 1 | 6 | 0 | 0 |
subtype4 | 0 | 1 | 2 | 0 |
subtype5 | 0 | 1 | 1 | 2 |
subtype6 | 1 | 2 | 1 | 0 |
subtype7 | 0 | 6 | 1 | 0 |
subtype8 | 0 | 4 | 1 | 1 |
P value = 0.136 (Fisher's exact test), Q value = 0.3
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 2 | 30 | 7 | 7 |
subtype1 | 0 | 6 | 1 | 1 |
subtype2 | 0 | 2 | 2 | 3 |
subtype3 | 1 | 6 | 0 | 0 |
subtype4 | 0 | 2 | 1 | 0 |
subtype5 | 0 | 1 | 1 | 2 |
subtype6 | 1 | 2 | 1 | 0 |
subtype7 | 0 | 6 | 0 | 1 |
subtype8 | 0 | 5 | 1 | 0 |
P value = 0.469 (Fisher's exact test), Q value = 0.63
nPatients | 0 | 1 |
---|---|---|
ALL | 40 | 6 |
subtype1 | 7 | 1 |
subtype2 | 5 | 2 |
subtype3 | 7 | 0 |
subtype4 | 2 | 1 |
subtype5 | 3 | 1 |
subtype6 | 4 | 0 |
subtype7 | 7 | 0 |
subtype8 | 5 | 1 |
P value = 0.468 (Fisher's exact test), Q value = 0.63
nPatients | FEMALE | MALE |
---|---|---|
ALL | 28 | 18 |
subtype1 | 6 | 2 |
subtype2 | 6 | 1 |
subtype3 | 3 | 4 |
subtype4 | 2 | 1 |
subtype5 | 3 | 1 |
subtype6 | 1 | 3 |
subtype7 | 3 | 4 |
subtype8 | 4 | 2 |
P value = 0.264 (Fisher's exact test), Q value = 0.42
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 1 | 1 | 35 |
subtype1 | 0 | 0 | 6 |
subtype2 | 0 | 0 | 7 |
subtype3 | 0 | 1 | 3 |
subtype4 | 0 | 0 | 3 |
subtype5 | 0 | 0 | 4 |
subtype6 | 0 | 0 | 2 |
subtype7 | 0 | 0 | 6 |
subtype8 | 1 | 0 | 4 |
P value = 0.758 (Fisher's exact test), Q value = 0.87
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 6 | 17 |
subtype1 | 2 | 3 |
subtype2 | 1 | 4 |
subtype3 | 1 | 1 |
subtype4 | 1 | 1 |
subtype5 | 1 | 2 |
subtype6 | 0 | 0 |
subtype7 | 0 | 2 |
subtype8 | 0 | 4 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 24 | 14 | 18 | 23 |
P value = 0.000309 (logrank test), Q value = 0.0065
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 79 | 27 | 4.1 - 153.6 (36.3) |
subtype1 | 24 | 15 | 4.1 - 152.2 (20.4) |
subtype2 | 14 | 6 | 6.8 - 153.6 (37.4) |
subtype3 | 18 | 5 | 12.0 - 119.1 (48.4) |
subtype4 | 23 | 1 | 18.1 - 121.2 (39.5) |
P value = 0.906 (Kruskal-Wallis (anova)), Q value = 0.99
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 79 | 46.7 (15.8) |
subtype1 | 24 | 46.7 (18.2) |
subtype2 | 14 | 47.3 (14.9) |
subtype3 | 18 | 44.7 (12.8) |
subtype4 | 23 | 47.9 (16.5) |
P value = 0.013 (Fisher's exact test), Q value = 0.061
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 9 | 37 | 16 | 15 |
subtype1 | 3 | 8 | 8 | 5 |
subtype2 | 0 | 6 | 2 | 6 |
subtype3 | 1 | 7 | 5 | 3 |
subtype4 | 5 | 16 | 1 | 1 |
P value = 0.0973 (Fisher's exact test), Q value = 0.24
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 9 | 42 | 8 | 18 |
subtype1 | 3 | 10 | 4 | 7 |
subtype2 | 0 | 8 | 2 | 4 |
subtype3 | 1 | 8 | 1 | 6 |
subtype4 | 5 | 16 | 1 | 1 |
P value = 0.0483 (Fisher's exact test), Q value = 0.15
nPatients | 0 | 1 |
---|---|---|
ALL | 68 | 9 |
subtype1 | 21 | 3 |
subtype2 | 10 | 4 |
subtype3 | 14 | 2 |
subtype4 | 23 | 0 |
P value = 0.239 (Fisher's exact test), Q value = 0.41
nPatients | FEMALE | MALE |
---|---|---|
ALL | 48 | 31 |
subtype1 | 16 | 8 |
subtype2 | 11 | 3 |
subtype3 | 8 | 10 |
subtype4 | 13 | 10 |
P value = 0.303 (Fisher's exact test), Q value = 0.47
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 1 | 1 | 66 |
subtype1 | 0 | 0 | 24 |
subtype2 | 0 | 0 | 12 |
subtype3 | 0 | 0 | 16 |
subtype4 | 1 | 1 | 14 |
P value = 0.944 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 7 | 30 |
subtype1 | 2 | 11 |
subtype2 | 2 | 7 |
subtype3 | 2 | 6 |
subtype4 | 1 | 6 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 23 | 24 | 7 | 25 |
P value = 0.000278 (logrank test), Q value = 0.0065
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 79 | 27 | 4.1 - 153.6 (36.3) |
subtype1 | 23 | 15 | 4.1 - 152.2 (33.8) |
subtype2 | 24 | 8 | 6.8 - 153.6 (41.0) |
subtype3 | 7 | 3 | 12.6 - 95.2 (20.2) |
subtype4 | 25 | 1 | 18.1 - 121.2 (39.5) |
P value = 0.623 (Kruskal-Wallis (anova)), Q value = 0.79
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 79 | 46.7 (15.8) |
subtype1 | 23 | 47.3 (19.2) |
subtype2 | 24 | 45.1 (14.7) |
subtype3 | 7 | 41.3 (14.9) |
subtype4 | 25 | 49.2 (13.8) |
P value = 0.00442 (Fisher's exact test), Q value = 0.029
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 9 | 37 | 16 | 15 |
subtype1 | 2 | 9 | 7 | 5 |
subtype2 | 0 | 9 | 5 | 8 |
subtype3 | 2 | 2 | 1 | 2 |
subtype4 | 5 | 17 | 3 | 0 |
P value = 0.0359 (Fisher's exact test), Q value = 0.12
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 9 | 42 | 8 | 18 |
subtype1 | 2 | 12 | 4 | 5 |
subtype2 | 0 | 11 | 2 | 9 |
subtype3 | 2 | 2 | 1 | 2 |
subtype4 | 5 | 17 | 1 | 2 |
P value = 0.0357 (Fisher's exact test), Q value = 0.12
nPatients | 0 | 1 |
---|---|---|
ALL | 68 | 9 |
subtype1 | 19 | 4 |
subtype2 | 17 | 5 |
subtype3 | 7 | 0 |
subtype4 | 25 | 0 |
P value = 0.359 (Fisher's exact test), Q value = 0.53
nPatients | FEMALE | MALE |
---|---|---|
ALL | 48 | 31 |
subtype1 | 17 | 6 |
subtype2 | 13 | 11 |
subtype3 | 5 | 2 |
subtype4 | 13 | 12 |
P value = 0.00924 (Fisher's exact test), Q value = 0.046
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 1 | 1 | 66 |
subtype1 | 0 | 0 | 22 |
subtype2 | 0 | 0 | 20 |
subtype3 | 1 | 1 | 5 |
subtype4 | 0 | 0 | 19 |
P value = 0.24 (Fisher's exact test), Q value = 0.41
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 7 | 30 |
subtype1 | 2 | 10 |
subtype2 | 3 | 9 |
subtype3 | 2 | 3 |
subtype4 | 0 | 8 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 38 | 16 | 26 |
P value = 0.00588 (logrank test), Q value = 0.031
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 80 | 28 | 4.1 - 153.6 (36.3) |
subtype1 | 38 | 16 | 4.1 - 127.5 (34.4) |
subtype2 | 16 | 9 | 12.6 - 153.6 (29.2) |
subtype3 | 26 | 3 | 18.1 - 121.2 (45.1) |
P value = 0.219 (Kruskal-Wallis (anova)), Q value = 0.41
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 46.4 (15.9) |
subtype1 | 38 | 43.0 (15.8) |
subtype2 | 16 | 50.1 (17.0) |
subtype3 | 26 | 49.0 (14.8) |
P value = 0.00051 (Fisher's exact test), Q value = 0.0065
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 9 | 37 | 16 | 16 |
subtype1 | 3 | 14 | 12 | 9 |
subtype2 | 1 | 5 | 2 | 7 |
subtype3 | 5 | 18 | 2 | 0 |
P value = 0.00531 (Fisher's exact test), Q value = 0.031
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 9 | 42 | 9 | 18 |
subtype1 | 3 | 18 | 4 | 13 |
subtype2 | 1 | 6 | 3 | 5 |
subtype3 | 5 | 18 | 2 | 0 |
P value = 0.0457 (Fisher's exact test), Q value = 0.15
nPatients | 0 | 1 |
---|---|---|
ALL | 68 | 10 |
subtype1 | 31 | 7 |
subtype2 | 12 | 3 |
subtype3 | 25 | 0 |
P value = 0.138 (Fisher's exact test), Q value = 0.3
nPatients | FEMALE | MALE |
---|---|---|
ALL | 49 | 31 |
subtype1 | 25 | 13 |
subtype2 | 12 | 4 |
subtype3 | 12 | 14 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 1 | 1 | 67 |
subtype1 | 1 | 1 | 33 |
subtype2 | 0 | 0 | 15 |
subtype3 | 0 | 0 | 19 |
P value = 0.385 (Fisher's exact test), Q value = 0.55
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 30 |
subtype1 | 5 | 18 |
subtype2 | 3 | 6 |
subtype3 | 0 | 6 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 17 | 27 | 12 | 20 | 4 |
P value = 0.0277 (logrank test), Q value = 0.11
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 80 | 28 | 4.1 - 153.6 (36.3) |
subtype1 | 17 | 8 | 4.1 - 100.2 (44.5) |
subtype2 | 27 | 7 | 12.6 - 153.6 (36.3) |
subtype3 | 12 | 0 | 18.1 - 119.1 (37.5) |
subtype4 | 20 | 11 | 5.2 - 152.2 (30.9) |
subtype5 | 4 | 2 | 38.5 - 53.0 (44.3) |
P value = 0.265 (Kruskal-Wallis (anova)), Q value = 0.42
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 46.4 (15.9) |
subtype1 | 17 | 46.3 (14.3) |
subtype2 | 27 | 47.7 (14.7) |
subtype3 | 12 | 40.5 (15.9) |
subtype4 | 20 | 45.4 (18.8) |
subtype5 | 4 | 60.8 (9.8) |
P value = 9e-04 (Fisher's exact test), Q value = 0.0081
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 9 | 37 | 16 | 16 |
subtype1 | 0 | 5 | 7 | 4 |
subtype2 | 2 | 19 | 0 | 6 |
subtype3 | 4 | 5 | 2 | 1 |
subtype4 | 3 | 6 | 7 | 3 |
subtype5 | 0 | 2 | 0 | 2 |
P value = 0.153 (Fisher's exact test), Q value = 0.32
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 9 | 42 | 9 | 18 |
subtype1 | 0 | 6 | 4 | 6 |
subtype2 | 2 | 19 | 1 | 5 |
subtype3 | 4 | 5 | 1 | 2 |
subtype4 | 3 | 9 | 3 | 4 |
subtype5 | 0 | 3 | 0 | 1 |
P value = 0.254 (Fisher's exact test), Q value = 0.42
nPatients | 0 | 1 |
---|---|---|
ALL | 68 | 10 |
subtype1 | 13 | 3 |
subtype2 | 25 | 2 |
subtype3 | 12 | 0 |
subtype4 | 15 | 4 |
subtype5 | 3 | 1 |
P value = 0.33 (Fisher's exact test), Q value = 0.5
nPatients | FEMALE | MALE |
---|---|---|
ALL | 49 | 31 |
subtype1 | 7 | 10 |
subtype2 | 16 | 11 |
subtype3 | 9 | 3 |
subtype4 | 14 | 6 |
subtype5 | 3 | 1 |
P value = 0.105 (Fisher's exact test), Q value = 0.25
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 1 | 1 | 67 |
subtype1 | 0 | 0 | 15 |
subtype2 | 0 | 0 | 23 |
subtype3 | 1 | 1 | 8 |
subtype4 | 0 | 0 | 18 |
subtype5 | 0 | 0 | 3 |
P value = 0.699 (Fisher's exact test), Q value = 0.85
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 30 |
subtype1 | 3 | 4 |
subtype2 | 2 | 8 |
subtype3 | 1 | 6 |
subtype4 | 2 | 9 |
subtype5 | 0 | 3 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 29 | 22 | 27 |
P value = 0.000208 (logrank test), Q value = 0.0065
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 78 | 28 | 4.1 - 153.6 (36.1) |
subtype1 | 29 | 10 | 4.1 - 152.2 (36.0) |
subtype2 | 22 | 14 | 5.2 - 153.6 (23.2) |
subtype3 | 27 | 4 | 18.1 - 121.2 (46.8) |
P value = 0.412 (Kruskal-Wallis (anova)), Q value = 0.57
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 46.8 (15.9) |
subtype1 | 29 | 45.4 (14.5) |
subtype2 | 22 | 44.2 (18.1) |
subtype3 | 27 | 50.3 (15.3) |
P value = 0.00057 (Fisher's exact test), Q value = 0.0065
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 9 | 35 | 16 | 16 |
subtype1 | 4 | 10 | 8 | 7 |
subtype2 | 0 | 7 | 5 | 9 |
subtype3 | 5 | 18 | 3 | 0 |
P value = 0.00091 (Fisher's exact test), Q value = 0.0081
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 9 | 40 | 9 | 18 |
subtype1 | 4 | 14 | 2 | 9 |
subtype2 | 0 | 8 | 4 | 9 |
subtype3 | 5 | 18 | 3 | 0 |
P value = 0.0276 (Fisher's exact test), Q value = 0.11
nPatients | 0 | 1 |
---|---|---|
ALL | 66 | 10 |
subtype1 | 23 | 6 |
subtype2 | 17 | 4 |
subtype3 | 26 | 0 |
P value = 0.0611 (Fisher's exact test), Q value = 0.18
nPatients | FEMALE | MALE |
---|---|---|
ALL | 49 | 29 |
subtype1 | 21 | 8 |
subtype2 | 16 | 6 |
subtype3 | 12 | 15 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 1 | 1 | 66 |
subtype1 | 1 | 1 | 25 |
subtype2 | 0 | 0 | 21 |
subtype3 | 0 | 0 | 20 |
P value = 0.866 (Fisher's exact test), Q value = 0.96
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 29 |
subtype1 | 3 | 14 |
subtype2 | 4 | 10 |
subtype3 | 1 | 5 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 40 | 24 | 14 |
P value = 0.0634 (logrank test), Q value = 0.18
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 78 | 28 | 4.1 - 153.6 (36.1) |
subtype1 | 40 | 19 | 4.1 - 152.2 (36.2) |
subtype2 | 24 | 5 | 12.8 - 153.6 (37.9) |
subtype3 | 14 | 4 | 12.6 - 100.2 (30.2) |
P value = 0.969 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 46.8 (15.9) |
subtype1 | 40 | 46.5 (16.4) |
subtype2 | 24 | 47.2 (15.4) |
subtype3 | 14 | 46.6 (16.1) |
P value = 0.00317 (Fisher's exact test), Q value = 0.025
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 9 | 35 | 16 | 16 |
subtype1 | 4 | 12 | 13 | 10 |
subtype2 | 2 | 18 | 0 | 4 |
subtype3 | 3 | 5 | 3 | 2 |
P value = 0.0907 (Fisher's exact test), Q value = 0.23
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 9 | 40 | 9 | 18 |
subtype1 | 4 | 17 | 5 | 13 |
subtype2 | 2 | 18 | 1 | 3 |
subtype3 | 3 | 5 | 3 | 2 |
P value = 0.155 (Fisher's exact test), Q value = 0.32
nPatients | 0 | 1 |
---|---|---|
ALL | 66 | 10 |
subtype1 | 31 | 8 |
subtype2 | 22 | 2 |
subtype3 | 13 | 0 |
P value = 0.363 (Fisher's exact test), Q value = 0.53
nPatients | FEMALE | MALE |
---|---|---|
ALL | 49 | 29 |
subtype1 | 28 | 12 |
subtype2 | 14 | 10 |
subtype3 | 7 | 7 |
P value = 0.408 (Fisher's exact test), Q value = 0.57
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 1 | 1 | 66 |
subtype1 | 0 | 1 | 35 |
subtype2 | 0 | 0 | 20 |
subtype3 | 1 | 0 | 11 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 29 |
subtype1 | 5 | 18 |
subtype2 | 2 | 7 |
subtype3 | 1 | 4 |
-
Cluster data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/ACC-TP/15087341/ACC-TP.mergedcluster.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ACC-TP/15074660/ACC-TP.merged_data.txt
-
Number of patients = 92
-
Number of clustering approaches = 10
-
Number of selected clinical features = 8
-
Exclude small clusters that include fewer than K patients, K = 3
consensus non-negative matrix factorization clustering approach (Brunet et al. 2004)
Resampling-based clustering method (Monti et al. 2003)
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For 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.