This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 8 different clustering approaches and 9 clinical features across 151 patients, 30 significant findings detected with P value < 0.05 and Q value < 0.25.
-
3 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes correlate to 'AGE' and 'RACE'.
-
3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'AGE', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', and 'RACE'.
-
CNMF clustering analysis on sequencing-based mRNA expression data identified 5 subtypes that correlate to 'AGE', 'PATHOLOGY.T.STAGE', and 'RACE'.
-
Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'AGE', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.M.STAGE', and 'RACE'.
-
3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'AGE', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', and 'RACE'.
-
4 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes correlate to 'Time to Death', 'AGE', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', and 'RACE'.
-
4 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes correlate to 'AGE', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', and 'RACE'.
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3 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes correlate to 'AGE', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', and 'RACE'.
Clinical Features |
Statistical Tests |
Copy Number Ratio CNMF subtypes |
METHLYATION CNMF |
RNAseq CNMF subtypes |
RNAseq cHierClus subtypes |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRseq Mature CNMF subtypes |
MIRseq Mature cHierClus subtypes |
Time to Death | logrank test |
0.0264 (1.00) |
0.168 (1.00) |
0.472 (1.00) |
0.431 (1.00) |
0.34 (1.00) |
0.00374 (0.168) |
0.02 (0.781) |
0.0772 (1.00) |
AGE | Kruskal-Wallis (anova) |
0.000396 (0.021) |
0.000742 (0.0363) |
0.000293 (0.0168) |
0.000843 (0.0405) |
8.2e-05 (0.00492) |
4e-05 (0.00244) |
0.00065 (0.0325) |
1.13e-05 (0.000724) |
NEOPLASM DISEASESTAGE | Fisher's exact test |
0.0484 (1.00) |
0.00029 (0.0168) |
0.0294 (1.00) |
0.00031 (0.0174) |
2e-05 (0.00126) |
0.0004 (0.021) |
0.0004 (0.021) |
3e-05 (0.00186) |
PATHOLOGY T STAGE | Fisher's exact test |
0.011 (0.461) |
0.00033 (0.0181) |
0.0056 (0.246) |
0.0123 (0.504) |
0.00015 (0.00885) |
0.00133 (0.0612) |
0.00116 (0.0545) |
0.00038 (0.0205) |
PATHOLOGY N STAGE | Fisher's exact test |
0.158 (1.00) |
0.212 (1.00) |
0.554 (1.00) |
0.0797 (1.00) |
0.112 (1.00) |
0.112 (1.00) |
0.12 (1.00) |
0.0126 (0.504) |
PATHOLOGY M STAGE | Fisher's exact test |
0.101 (1.00) |
0.465 (1.00) |
0.15 (1.00) |
0.00565 (0.246) |
0.139 (1.00) |
0.186 (1.00) |
0.113 (1.00) |
0.0923 (1.00) |
GENDER | Fisher's exact test |
0.0963 (1.00) |
1 (1.00) |
0.361 (1.00) |
0.234 (1.00) |
1 (1.00) |
0.638 (1.00) |
0.282 (1.00) |
0.945 (1.00) |
NUMBERPACKYEARSSMOKED | Kruskal-Wallis (anova) |
0.463 (1.00) |
0.187 (1.00) |
0.781 (1.00) |
0.676 (1.00) |
0.115 (1.00) |
0.636 (1.00) |
0.117 (1.00) |
0.134 (1.00) |
RACE | Fisher's exact test |
1e-05 (0.00072) |
1e-05 (0.00072) |
1e-05 (0.00072) |
1e-05 (0.00072) |
1e-05 (0.00072) |
1e-05 (0.00072) |
1e-05 (0.00072) |
1e-05 (0.00072) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 59 | 35 | 56 |
P value = 0.0264 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 142 | 54 | 0.0 - 122.1 (7.5) |
subtype1 | 59 | 28 | 0.1 - 122.1 (8.9) |
subtype2 | 34 | 9 | 0.1 - 83.2 (9.0) |
subtype3 | 49 | 17 | 0.0 - 52.6 (0.5) |
P value = 0.000396 (Kruskal-Wallis (anova)), Q value = 0.021
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 150 | 63.2 (12.5) |
subtype1 | 59 | 64.1 (12.8) |
subtype2 | 35 | 69.0 (12.0) |
subtype3 | 56 | 58.7 (10.8) |
P value = 0.0484 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 8 | 4 | 6 | 1 | 35 | 26 | 23 | 11 | 8 | 6 | 3 | 2 |
subtype1 | 4 | 2 | 2 | 0 | 5 | 11 | 12 | 3 | 3 | 2 | 2 | 1 |
subtype2 | 4 | 1 | 1 | 0 | 9 | 7 | 2 | 2 | 1 | 3 | 0 | 1 |
subtype3 | 0 | 1 | 3 | 1 | 21 | 8 | 9 | 6 | 4 | 1 | 1 | 0 |
P value = 0.011 (Fisher's exact test), Q value = 0.46
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 26 | 33 | 74 | 4 |
subtype1 | 15 | 7 | 29 | 0 |
subtype2 | 7 | 7 | 16 | 1 |
subtype3 | 4 | 19 | 29 | 3 |
P value = 0.158 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 64 | 54 | 11 | 6 |
subtype1 | 18 | 26 | 5 | 2 |
subtype2 | 17 | 9 | 1 | 3 |
subtype3 | 29 | 19 | 5 | 1 |
P value = 0.101 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | M1A | MX |
---|---|---|---|---|
ALL | 111 | 2 | 3 | 17 |
subtype1 | 36 | 1 | 2 | 10 |
subtype2 | 25 | 0 | 1 | 4 |
subtype3 | 50 | 1 | 0 | 3 |
P value = 0.0963 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 21 | 129 |
subtype1 | 6 | 53 |
subtype2 | 9 | 26 |
subtype3 | 6 | 50 |
P value = 0.463 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 81 | 35.2 (21.3) |
subtype1 | 29 | 35.5 (22.4) |
subtype2 | 17 | 40.5 (23.6) |
subtype3 | 35 | 32.4 (19.2) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00072
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 38 | 2 | 93 |
subtype1 | 4 | 0 | 40 |
subtype2 | 3 | 1 | 30 |
subtype3 | 31 | 1 | 23 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 68 | 28 | 55 |
P value = 0.168 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 143 | 55 | 0.0 - 122.1 (7.6) |
subtype1 | 68 | 29 | 0.3 - 122.1 (8.9) |
subtype2 | 26 | 8 | 0.0 - 83.2 (7.9) |
subtype3 | 49 | 18 | 0.1 - 68.0 (2.6) |
P value = 0.000742 (Kruskal-Wallis (anova)), Q value = 0.036
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 151 | 63.3 (12.4) |
subtype1 | 68 | 66.1 (12.1) |
subtype2 | 28 | 65.6 (14.3) |
subtype3 | 55 | 58.5 (10.4) |
P value = 0.00029 (Fisher's exact test), Q value = 0.017
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 8 | 4 | 6 | 1 | 35 | 26 | 24 | 11 | 8 | 6 | 3 | 2 |
subtype1 | 8 | 2 | 2 | 0 | 4 | 13 | 13 | 2 | 4 | 4 | 2 | 1 |
subtype2 | 0 | 1 | 2 | 0 | 7 | 5 | 3 | 5 | 0 | 1 | 0 | 1 |
subtype3 | 0 | 1 | 2 | 1 | 24 | 8 | 8 | 4 | 4 | 1 | 1 | 0 |
P value = 0.00033 (Fisher's exact test), Q value = 0.018
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 26 | 33 | 75 | 4 |
subtype1 | 20 | 7 | 31 | 0 |
subtype2 | 2 | 7 | 15 | 2 |
subtype3 | 4 | 19 | 29 | 2 |
P value = 0.212 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 64 | 55 | 11 | 6 |
subtype1 | 21 | 29 | 4 | 4 |
subtype2 | 11 | 10 | 2 | 1 |
subtype3 | 32 | 16 | 5 | 1 |
P value = 0.465 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | M1A | MX |
---|---|---|---|---|
ALL | 112 | 2 | 3 | 17 |
subtype1 | 43 | 1 | 2 | 9 |
subtype2 | 21 | 0 | 1 | 4 |
subtype3 | 48 | 1 | 0 | 4 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 21 | 130 |
subtype1 | 9 | 59 |
subtype2 | 4 | 24 |
subtype3 | 8 | 47 |
P value = 0.187 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 81 | 35.2 (21.3) |
subtype1 | 32 | 40.5 (23.9) |
subtype2 | 16 | 35.4 (19.8) |
subtype3 | 33 | 30.1 (18.4) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00072
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 38 | 2 | 93 |
subtype1 | 1 | 0 | 53 |
subtype2 | 7 | 0 | 19 |
subtype3 | 30 | 2 | 21 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 43 | 8 | 18 | 29 | 10 |
P value = 0.472 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 101 | 34 | 0.0 - 122.1 (4.9) |
subtype1 | 43 | 16 | 0.3 - 122.1 (7.1) |
subtype2 | 8 | 2 | 0.0 - 54.0 (7.5) |
subtype3 | 15 | 5 | 0.1 - 44.8 (0.5) |
subtype4 | 26 | 9 | 0.1 - 68.0 (0.4) |
subtype5 | 9 | 2 | 0.1 - 23.4 (2.6) |
P value = 0.000293 (Kruskal-Wallis (anova)), Q value = 0.017
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 108 | 62.5 (12.5) |
subtype1 | 43 | 67.8 (12.6) |
subtype2 | 8 | 65.4 (13.3) |
subtype3 | 18 | 57.5 (11.1) |
subtype4 | 29 | 60.1 (11.0) |
subtype5 | 10 | 53.3 (7.1) |
P value = 0.0294 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 7 | 4 | 4 | 1 | 30 | 17 | 11 | 8 | 7 | 3 | 2 |
subtype1 | 7 | 2 | 1 | 0 | 3 | 7 | 2 | 2 | 2 | 3 | 1 |
subtype2 | 0 | 1 | 0 | 0 | 2 | 2 | 0 | 1 | 1 | 0 | 0 |
subtype3 | 0 | 1 | 1 | 0 | 7 | 2 | 4 | 0 | 3 | 0 | 0 |
subtype4 | 0 | 0 | 2 | 1 | 13 | 5 | 4 | 2 | 1 | 0 | 1 |
subtype5 | 0 | 0 | 0 | 0 | 5 | 1 | 1 | 3 | 0 | 0 | 0 |
P value = 0.0056 (Fisher's exact test), Q value = 0.25
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 20 | 26 | 49 | 3 |
subtype1 | 15 | 6 | 13 | 0 |
subtype2 | 1 | 3 | 3 | 0 |
subtype3 | 2 | 4 | 12 | 0 |
subtype4 | 2 | 10 | 16 | 1 |
subtype5 | 0 | 3 | 5 | 2 |
P value = 0.554 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 51 | 34 | 9 | 3 |
subtype1 | 14 | 13 | 4 | 3 |
subtype2 | 3 | 3 | 1 | 0 |
subtype3 | 9 | 6 | 3 | 0 |
subtype4 | 18 | 10 | 1 | 0 |
subtype5 | 7 | 2 | 0 | 0 |
P value = 0.15 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | M1A | MX |
---|---|---|---|---|
ALL | 77 | 1 | 1 | 15 |
subtype1 | 20 | 0 | 1 | 10 |
subtype2 | 7 | 0 | 0 | 0 |
subtype3 | 16 | 0 | 0 | 1 |
subtype4 | 25 | 1 | 0 | 3 |
subtype5 | 9 | 0 | 0 | 1 |
P value = 0.361 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 16 | 92 |
subtype1 | 9 | 34 |
subtype2 | 0 | 8 |
subtype3 | 3 | 15 |
subtype4 | 2 | 27 |
subtype5 | 2 | 8 |
P value = 0.781 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 65 | 35.7 (19.8) |
subtype1 | 25 | 35.5 (19.9) |
subtype2 | 7 | 43.2 (20.7) |
subtype3 | 10 | 35.7 (25.7) |
subtype4 | 20 | 33.0 (17.1) |
subtype5 | 3 | 37.5 (22.5) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00072
nPatients | ASIAN | WHITE |
---|---|---|
ALL | 36 | 68 |
subtype1 | 0 | 39 |
subtype2 | 1 | 7 |
subtype3 | 12 | 6 |
subtype4 | 18 | 11 |
subtype5 | 5 | 5 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 36 | 60 | 12 |
P value = 0.431 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 101 | 34 | 0.0 - 122.1 (4.9) |
subtype1 | 36 | 14 | 0.3 - 122.1 (7.8) |
subtype2 | 53 | 17 | 0.0 - 68.0 (0.5) |
subtype3 | 12 | 3 | 0.4 - 54.0 (4.5) |
P value = 0.000843 (Kruskal-Wallis (anova)), Q value = 0.04
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 108 | 62.5 (12.5) |
subtype1 | 36 | 67.9 (11.8) |
subtype2 | 60 | 58.8 (10.9) |
subtype3 | 12 | 65.0 (15.8) |
P value = 0.00031 (Fisher's exact test), Q value = 0.017
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 7 | 4 | 4 | 1 | 30 | 17 | 11 | 8 | 7 | 3 | 2 |
subtype1 | 5 | 2 | 1 | 0 | 4 | 7 | 1 | 3 | 1 | 3 | 1 |
subtype2 | 0 | 2 | 3 | 1 | 26 | 9 | 9 | 5 | 4 | 0 | 1 |
subtype3 | 2 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 2 | 0 | 0 |
P value = 0.0123 (Fisher's exact test), Q value = 0.5
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 20 | 26 | 49 | 3 |
subtype1 | 11 | 6 | 12 | 1 |
subtype2 | 5 | 19 | 34 | 2 |
subtype3 | 4 | 1 | 3 | 0 |
P value = 0.0797 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 51 | 34 | 9 | 3 |
subtype1 | 12 | 11 | 3 | 3 |
subtype2 | 36 | 20 | 4 | 0 |
subtype3 | 3 | 3 | 2 | 0 |
P value = 0.00565 (Fisher's exact test), Q value = 0.25
nPatients | M0 | M1 | M1A | MX |
---|---|---|---|---|
ALL | 77 | 1 | 1 | 15 |
subtype1 | 19 | 0 | 1 | 8 |
subtype2 | 54 | 1 | 0 | 4 |
subtype3 | 4 | 0 | 0 | 3 |
P value = 0.234 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 16 | 92 |
subtype1 | 8 | 28 |
subtype2 | 6 | 54 |
subtype3 | 2 | 10 |
P value = 0.676 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 65 | 35.7 (19.8) |
subtype1 | 18 | 35.7 (22.4) |
subtype2 | 37 | 34.6 (19.1) |
subtype3 | 10 | 39.8 (18.9) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00072
nPatients | ASIAN | WHITE |
---|---|---|
ALL | 36 | 68 |
subtype1 | 0 | 33 |
subtype2 | 36 | 24 |
subtype3 | 0 | 11 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 76 | 63 | 11 |
P value = 0.34 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 142 | 55 | 0.0 - 122.1 (7.6) |
subtype1 | 76 | 33 | 0.3 - 122.1 (8.9) |
subtype2 | 56 | 20 | 0.0 - 68.0 (2.3) |
subtype3 | 10 | 2 | 0.1 - 20.8 (6.6) |
P value = 8.2e-05 (Kruskal-Wallis (anova)), Q value = 0.0049
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 150 | 63.4 (12.4) |
subtype1 | 76 | 67.0 (12.2) |
subtype2 | 63 | 58.4 (10.7) |
subtype3 | 11 | 66.3 (13.8) |
P value = 2e-05 (Fisher's exact test), Q value = 0.0013
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 8 | 4 | 6 | 1 | 34 | 26 | 24 | 11 | 8 | 6 | 3 | 2 |
subtype1 | 8 | 2 | 2 | 0 | 5 | 15 | 13 | 2 | 4 | 5 | 2 | 2 |
subtype2 | 0 | 1 | 3 | 1 | 27 | 9 | 10 | 5 | 4 | 1 | 1 | 0 |
subtype3 | 0 | 1 | 1 | 0 | 2 | 2 | 1 | 4 | 0 | 0 | 0 | 0 |
P value = 0.00015 (Fisher's exact test), Q value = 0.0088
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 26 | 33 | 74 | 4 |
subtype1 | 21 | 10 | 33 | 0 |
subtype2 | 4 | 21 | 35 | 2 |
subtype3 | 1 | 2 | 6 | 2 |
P value = 0.112 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 63 | 55 | 11 | 6 |
subtype1 | 22 | 31 | 6 | 5 |
subtype2 | 36 | 19 | 5 | 1 |
subtype3 | 5 | 5 | 0 | 0 |
P value = 0.139 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | M1A | MX |
---|---|---|---|---|
ALL | 111 | 2 | 3 | 17 |
subtype1 | 46 | 1 | 3 | 11 |
subtype2 | 56 | 1 | 0 | 4 |
subtype3 | 9 | 0 | 0 | 2 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 21 | 129 |
subtype1 | 11 | 65 |
subtype2 | 9 | 54 |
subtype3 | 1 | 10 |
P value = 0.115 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 35.5 (21.3) |
subtype1 | 34 | 39.2 (24.1) |
subtype2 | 39 | 30.0 (15.7) |
subtype3 | 7 | 48.1 (27.4) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00072
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 37 | 2 | 93 |
subtype1 | 1 | 0 | 59 |
subtype2 | 34 | 2 | 25 |
subtype3 | 2 | 0 | 9 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 56 | 24 | 46 | 24 |
P value = 0.00374 (logrank test), Q value = 0.17
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 142 | 55 | 0.0 - 122.1 (7.6) |
subtype1 | 56 | 28 | 0.3 - 122.1 (8.1) |
subtype2 | 24 | 6 | 3.0 - 83.2 (14.1) |
subtype3 | 41 | 16 | 0.0 - 33.3 (1.0) |
subtype4 | 21 | 5 | 0.1 - 68.0 (4.1) |
P value = 4e-05 (Kruskal-Wallis (anova)), Q value = 0.0024
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 150 | 63.4 (12.4) |
subtype1 | 56 | 65.2 (12.2) |
subtype2 | 24 | 71.8 (11.7) |
subtype3 | 46 | 58.3 (11.9) |
subtype4 | 24 | 60.5 (9.0) |
P value = 4e-04 (Fisher's exact test), Q value = 0.021
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 8 | 4 | 6 | 1 | 34 | 26 | 24 | 11 | 8 | 6 | 3 | 2 |
subtype1 | 7 | 2 | 2 | 0 | 1 | 10 | 11 | 1 | 3 | 3 | 1 | 2 |
subtype2 | 1 | 0 | 0 | 0 | 4 | 6 | 3 | 3 | 1 | 2 | 1 | 0 |
subtype3 | 0 | 1 | 2 | 1 | 16 | 8 | 8 | 5 | 3 | 1 | 0 | 0 |
subtype4 | 0 | 1 | 2 | 0 | 13 | 2 | 2 | 2 | 1 | 0 | 1 | 0 |
P value = 0.00133 (Fisher's exact test), Q value = 0.061
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 26 | 33 | 74 | 4 |
subtype1 | 18 | 8 | 20 | 0 |
subtype2 | 3 | 3 | 15 | 1 |
subtype3 | 2 | 13 | 27 | 3 |
subtype4 | 3 | 9 | 12 | 0 |
P value = 0.112 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 63 | 55 | 11 | 6 |
subtype1 | 14 | 25 | 4 | 3 |
subtype2 | 8 | 9 | 2 | 2 |
subtype3 | 25 | 14 | 4 | 1 |
subtype4 | 16 | 7 | 1 | 0 |
P value = 0.186 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | M1A | MX |
---|---|---|---|---|
ALL | 111 | 2 | 3 | 17 |
subtype1 | 31 | 1 | 2 | 9 |
subtype2 | 18 | 0 | 1 | 3 |
subtype3 | 41 | 0 | 0 | 4 |
subtype4 | 21 | 1 | 0 | 1 |
P value = 0.638 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 21 | 129 |
subtype1 | 7 | 49 |
subtype2 | 5 | 19 |
subtype3 | 5 | 41 |
subtype4 | 4 | 20 |
P value = 0.636 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 35.5 (21.3) |
subtype1 | 24 | 34.7 (18.9) |
subtype2 | 11 | 46.9 (32.1) |
subtype3 | 28 | 34.6 (19.8) |
subtype4 | 17 | 30.7 (17.4) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00072
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 37 | 2 | 93 |
subtype1 | 1 | 0 | 42 |
subtype2 | 0 | 0 | 20 |
subtype3 | 22 | 2 | 21 |
subtype4 | 14 | 0 | 10 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 60 | 47 | 32 | 7 |
P value = 0.02 (logrank test), Q value = 0.78
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 138 | 55 | 0.0 - 122.1 (7.6) |
subtype1 | 60 | 28 | 0.3 - 122.1 (8.7) |
subtype2 | 41 | 17 | 0.0 - 44.8 (0.8) |
subtype3 | 30 | 7 | 0.1 - 83.2 (13.5) |
subtype4 | 7 | 3 | 0.8 - 68.0 (12.0) |
P value = 0.00065 (Kruskal-Wallis (anova)), Q value = 0.033
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 146 | 63.3 (12.5) |
subtype1 | 60 | 66.3 (12.9) |
subtype2 | 47 | 57.4 (10.6) |
subtype3 | 32 | 66.8 (12.4) |
subtype4 | 7 | 62.0 (9.2) |
P value = 4e-04 (Fisher's exact test), Q value = 0.021
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 7 | 4 | 5 | 1 | 34 | 25 | 23 | 11 | 8 | 6 | 3 | 2 |
subtype1 | 7 | 2 | 2 | 0 | 2 | 11 | 11 | 2 | 3 | 2 | 2 | 2 |
subtype2 | 0 | 1 | 2 | 1 | 20 | 8 | 7 | 1 | 4 | 1 | 1 | 0 |
subtype3 | 0 | 1 | 1 | 0 | 11 | 6 | 4 | 6 | 1 | 2 | 0 | 0 |
subtype4 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 2 | 0 | 1 | 0 | 0 |
P value = 0.00116 (Fisher's exact test), Q value = 0.055
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 25 | 32 | 72 | 4 |
subtype1 | 18 | 8 | 24 | 0 |
subtype2 | 4 | 16 | 26 | 0 |
subtype3 | 3 | 7 | 19 | 3 |
subtype4 | 0 | 1 | 3 | 1 |
P value = 0.12 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 60 | 54 | 11 | 6 |
subtype1 | 16 | 27 | 5 | 2 |
subtype2 | 25 | 15 | 4 | 1 |
subtype3 | 17 | 11 | 1 | 2 |
subtype4 | 2 | 1 | 1 | 1 |
P value = 0.113 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | M1A | MX |
---|---|---|---|---|
ALL | 108 | 2 | 3 | 16 |
subtype1 | 34 | 1 | 3 | 10 |
subtype2 | 41 | 1 | 0 | 3 |
subtype3 | 29 | 0 | 0 | 2 |
subtype4 | 4 | 0 | 0 | 1 |
P value = 0.282 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 19 | 127 |
subtype1 | 10 | 50 |
subtype2 | 4 | 43 |
subtype3 | 3 | 29 |
subtype4 | 2 | 5 |
P value = 0.117 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 35.6 (21.6) |
subtype1 | 28 | 35.0 (18.8) |
subtype2 | 29 | 28.6 (16.1) |
subtype3 | 18 | 46.5 (28.0) |
subtype4 | 3 | 43.3 (30.6) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00072
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 36 | 1 | 91 |
subtype1 | 1 | 0 | 44 |
subtype2 | 28 | 1 | 16 |
subtype3 | 6 | 0 | 25 |
subtype4 | 1 | 0 | 6 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 57 | 20 | 69 |
P value = 0.0772 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 138 | 55 | 0.0 - 122.1 (7.6) |
subtype1 | 57 | 29 | 0.3 - 122.1 (8.7) |
subtype2 | 20 | 5 | 3.0 - 83.2 (14.4) |
subtype3 | 61 | 21 | 0.0 - 68.0 (2.6) |
P value = 1.13e-05 (Kruskal-Wallis (anova)), Q value = 0.00072
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 146 | 63.3 (12.5) |
subtype1 | 57 | 65.0 (12.6) |
subtype2 | 20 | 73.0 (9.1) |
subtype3 | 69 | 59.2 (11.6) |
P value = 3e-05 (Fisher's exact test), Q value = 0.0019
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 7 | 4 | 5 | 1 | 34 | 25 | 23 | 11 | 8 | 6 | 3 | 2 |
subtype1 | 6 | 2 | 2 | 0 | 1 | 11 | 12 | 1 | 3 | 3 | 1 | 2 |
subtype2 | 1 | 0 | 0 | 0 | 4 | 4 | 2 | 2 | 1 | 2 | 1 | 0 |
subtype3 | 0 | 2 | 3 | 1 | 29 | 10 | 9 | 8 | 4 | 1 | 1 | 0 |
P value = 0.00038 (Fisher's exact test), Q value = 0.021
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 25 | 32 | 72 | 4 |
subtype1 | 18 | 8 | 21 | 0 |
subtype2 | 2 | 2 | 14 | 0 |
subtype3 | 5 | 22 | 37 | 4 |
P value = 0.0126 (Fisher's exact test), Q value = 0.5
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 60 | 54 | 11 | 6 |
subtype1 | 13 | 27 | 4 | 3 |
subtype2 | 8 | 6 | 2 | 2 |
subtype3 | 39 | 21 | 5 | 1 |
P value = 0.0923 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | M1A | MX |
---|---|---|---|---|
ALL | 108 | 2 | 3 | 16 |
subtype1 | 32 | 1 | 2 | 9 |
subtype2 | 15 | 0 | 1 | 2 |
subtype3 | 61 | 1 | 0 | 5 |
P value = 0.945 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 19 | 127 |
subtype1 | 7 | 50 |
subtype2 | 3 | 17 |
subtype3 | 9 | 60 |
P value = 0.134 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 78 | 35.6 (21.6) |
subtype1 | 25 | 34.0 (18.9) |
subtype2 | 9 | 53.7 (31.7) |
subtype3 | 44 | 32.8 (19.2) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00072
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 36 | 1 | 91 |
subtype1 | 1 | 0 | 41 |
subtype2 | 0 | 0 | 18 |
subtype3 | 35 | 1 | 32 |
-
Cluster data file = ESCA-TP.mergedcluster.txt
-
Clinical data file = ESCA-TP.merged_data.txt
-
Number of patients = 151
-
Number of clustering approaches = 8
-
Number of selected clinical features = 9
-
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.