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 127 patients, 25 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 '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 4 subtypes that correlate to 'AGE' and 'RACE'.
-
Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that correlate to 'AGE' 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 'AGE', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', and 'RACE'.
-
3 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes correlate to 'AGE', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', and 'RACE'.
-
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 |
0.528 (1.00) |
0.393 (1.00) |
0.638 (1.00) |
0.666 (1.00) |
0.413 (1.00) |
0.237 (1.00) |
0.455 (1.00) |
0.16 (1.00) |
AGE | Kruskal-Wallis (anova) |
0.0216 (0.952) |
0.000234 (0.0129) |
0.000228 (0.0128) |
0.0017 (0.0817) |
9.65e-06 (0.000695) |
0.000158 (0.00918) |
2.45e-05 (0.00154) |
0.000356 (0.0192) |
NEOPLASM DISEASESTAGE | Fisher's exact test |
0.324 (1.00) |
0.00015 (0.00885) |
0.022 (0.952) |
0.0228 (0.959) |
5e-05 (0.0031) |
0.0015 (0.0735) |
0.00066 (0.0343) |
5e-05 (0.0031) |
PATHOLOGY T STAGE | Fisher's exact test |
0.0676 (1.00) |
0.00036 (0.0192) |
0.0168 (0.757) |
0.00688 (0.323) |
0.00142 (0.071) |
0.00017 (0.00969) |
0.00092 (0.0469) |
6e-05 (0.0036) |
PATHOLOGY N STAGE | Fisher's exact test |
0.466 (1.00) |
0.263 (1.00) |
0.0681 (1.00) |
0.251 (1.00) |
0.129 (1.00) |
0.184 (1.00) |
0.135 (1.00) |
0.0261 (1.00) |
PATHOLOGY M STAGE | Fisher's exact test |
0.174 (1.00) |
0.157 (1.00) |
0.0875 (1.00) |
0.127 (1.00) |
0.0507 (1.00) |
0.0805 (1.00) |
0.0354 (1.00) |
0.0131 (0.604) |
GENDER | Fisher's exact test |
0.0979 (1.00) |
0.846 (1.00) |
0.0892 (1.00) |
0.138 (1.00) |
0.587 (1.00) |
0.55 (1.00) |
0.3 (1.00) |
0.322 (1.00) |
NUMBERPACKYEARSSMOKED | Kruskal-Wallis (anova) |
0.042 (1.00) |
0.36 (1.00) |
0.602 (1.00) |
0.675 (1.00) |
0.318 (1.00) |
0.698 (1.00) |
0.132 (1.00) |
0.251 (1.00) |
RACE | Fisher's exact test |
1e-05 (0.00071) |
1e-05 (0.00071) |
1e-05 (0.00071) |
1e-05 (0.00071) |
1e-05 (0.00071) |
1e-05 (0.00071) |
1e-05 (0.00071) |
1e-05 (0.00071) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 37 | 36 | 32 |
P value = 0.528 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 98 | 31 | 0.0 - 122.1 (4.2) |
subtype1 | 35 | 12 | 0.1 - 122.1 (7.0) |
subtype2 | 32 | 6 | 0.0 - 44.8 (0.2) |
subtype3 | 31 | 13 | 0.1 - 60.4 (5.1) |
P value = 0.0216 (Kruskal-Wallis (anova)), Q value = 0.95
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 105 | 62.6 (12.6) |
subtype1 | 37 | 67.1 (11.8) |
subtype2 | 36 | 59.1 (11.3) |
subtype3 | 32 | 61.5 (13.6) |
P value = 0.324 (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 | 16 | 11 | 8 | 6 | 3 | 1 |
subtype1 | 4 | 2 | 1 | 0 | 10 | 4 | 2 | 4 | 1 | 2 | 0 |
subtype2 | 0 | 1 | 2 | 1 | 16 | 7 | 5 | 2 | 2 | 0 | 0 |
subtype3 | 3 | 1 | 1 | 0 | 4 | 5 | 4 | 2 | 3 | 1 | 1 |
P value = 0.0676 (Fisher's exact test), Q value = 1
nPatients | T0+T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 19 | 26 | 50 |
subtype1 | 9 | 5 | 18 |
subtype2 | 3 | 15 | 18 |
subtype3 | 7 | 6 | 14 |
P value = 0.466 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 50 | 33 | 8 | 3 |
subtype1 | 18 | 9 | 2 | 2 |
subtype2 | 21 | 13 | 2 | 0 |
subtype3 | 11 | 11 | 4 | 1 |
P value = 0.174 (Fisher's exact test), Q value = 1
nPatients | M0 | M1A | MX |
---|---|---|---|
ALL | 75 | 1 | 15 |
subtype1 | 25 | 0 | 6 |
subtype2 | 32 | 0 | 3 |
subtype3 | 18 | 1 | 6 |
P value = 0.0979 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 15 | 90 |
subtype1 | 9 | 28 |
subtype2 | 4 | 32 |
subtype3 | 2 | 30 |
P value = 0.042 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 63 | 36.5 (19.6) |
subtype1 | 22 | 43.8 (22.4) |
subtype2 | 23 | 35.2 (18.4) |
subtype3 | 18 | 29.3 (14.6) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00071
nPatients | ASIAN | WHITE |
---|---|---|
ALL | 35 | 66 |
subtype1 | 5 | 29 |
subtype2 | 24 | 12 |
subtype3 | 6 | 25 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 55 | 24 | 48 |
P value = 0.393 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 119 | 38 | 0.0 - 122.1 (5.4) |
subtype1 | 55 | 19 | 0.3 - 122.1 (8.0) |
subtype2 | 22 | 7 | 0.0 - 83.2 (4.8) |
subtype3 | 42 | 12 | 0.1 - 53.9 (0.5) |
P value = 0.000234 (Kruskal-Wallis (anova)), Q value = 0.013
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 127 | 63.6 (12.7) |
subtype1 | 55 | 67.5 (11.8) |
subtype2 | 24 | 65.6 (15.2) |
subtype3 | 48 | 58.2 (10.5) |
P value = 0.00015 (Fisher's exact test), Q value = 0.0088
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 | 22 | 16 | 8 | 6 | 4 | 2 | 1 |
subtype1 | 7 | 2 | 2 | 0 | 3 | 11 | 7 | 1 | 3 | 3 | 2 | 1 |
subtype2 | 0 | 1 | 2 | 0 | 7 | 3 | 3 | 4 | 0 | 1 | 0 | 0 |
subtype3 | 0 | 1 | 1 | 1 | 24 | 8 | 6 | 3 | 3 | 0 | 0 | 0 |
P value = 0.00036 (Fisher's exact test), Q value = 0.019
nPatients | T0+T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 21 | 30 | 63 |
subtype1 | 17 | 6 | 22 |
subtype2 | 1 | 7 | 14 |
subtype3 | 3 | 17 | 27 |
P value = 0.263 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 59 | 41 | 8 | 4 |
subtype1 | 19 | 20 | 3 | 3 |
subtype2 | 10 | 7 | 2 | 1 |
subtype3 | 30 | 14 | 3 | 0 |
P value = 0.157 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | M1A | MX |
---|---|---|---|---|
ALL | 90 | 1 | 2 | 17 |
subtype1 | 30 | 1 | 2 | 9 |
subtype2 | 18 | 0 | 0 | 4 |
subtype3 | 42 | 0 | 0 | 4 |
P value = 0.846 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 18 | 109 |
subtype1 | 9 | 46 |
subtype2 | 3 | 21 |
subtype3 | 6 | 42 |
P value = 0.36 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 75 | 36.7 (21.2) |
subtype1 | 32 | 40.5 (23.9) |
subtype2 | 15 | 36.8 (19.5) |
subtype3 | 28 | 32.3 (18.6) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00071
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 36 | 2 | 84 |
subtype1 | 0 | 0 | 51 |
subtype2 | 7 | 0 | 16 |
subtype3 | 29 | 2 | 17 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 13 | 23 | 6 | 24 |
P value = 0.638 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 64 | 20 | 0.0 - 33.3 (3.2) |
subtype1 | 12 | 5 | 0.1 - 33.3 (0.3) |
subtype2 | 22 | 4 | 0.1 - 20.1 (0.1) |
subtype3 | 6 | 1 | 0.0 - 20.1 (2.0) |
subtype4 | 24 | 10 | 0.3 - 30.7 (6.8) |
P value = 0.000228 (Kruskal-Wallis (anova)), Q value = 0.013
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 66 | 62.1 (13.2) |
subtype1 | 13 | 58.2 (10.7) |
subtype2 | 23 | 57.9 (11.6) |
subtype3 | 6 | 50.5 (13.4) |
subtype4 | 24 | 71.1 (10.7) |
P value = 0.022 (Fisher's exact test), Q value = 0.95
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 4 | 3 | 2 | 1 | 21 | 10 | 6 | 6 | 5 | 1 | 1 |
subtype1 | 0 | 1 | 0 | 0 | 9 | 0 | 1 | 1 | 1 | 0 | 0 |
subtype2 | 0 | 0 | 2 | 1 | 9 | 4 | 4 | 2 | 1 | 0 | 0 |
subtype3 | 0 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 0 | 0 |
subtype4 | 4 | 2 | 0 | 0 | 2 | 5 | 0 | 2 | 2 | 1 | 1 |
P value = 0.0168 (Fisher's exact test), Q value = 0.76
nPatients | T0+T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 9 | 16 | 36 |
subtype1 | 1 | 3 | 9 |
subtype2 | 0 | 8 | 15 |
subtype3 | 0 | 1 | 4 |
subtype4 | 8 | 4 | 8 |
P value = 0.0681 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 35 | 18 | 7 | 1 |
subtype1 | 11 | 1 | 1 | 0 |
subtype2 | 15 | 7 | 1 | 0 |
subtype3 | 1 | 3 | 1 | 0 |
subtype4 | 8 | 7 | 4 | 1 |
P value = 0.0875 (Fisher's exact test), Q value = 1
nPatients | M0 | M1A | MX |
---|---|---|---|
ALL | 49 | 1 | 7 |
subtype1 | 12 | 0 | 0 |
subtype2 | 21 | 0 | 2 |
subtype3 | 5 | 0 | 0 |
subtype4 | 11 | 1 | 5 |
P value = 0.0892 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 10 | 56 |
subtype1 | 2 | 11 |
subtype2 | 1 | 22 |
subtype3 | 0 | 6 |
subtype4 | 7 | 17 |
P value = 0.602 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 41 | 36.8 (20.8) |
subtype1 | 6 | 49.1 (29.6) |
subtype2 | 15 | 35.7 (16.4) |
subtype3 | 5 | 37.2 (24.6) |
subtype4 | 15 | 33.0 (20.0) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00071
nPatients | ASIAN | WHITE |
---|---|---|
ALL | 27 | 36 |
subtype1 | 8 | 5 |
subtype2 | 17 | 6 |
subtype3 | 2 | 4 |
subtype4 | 0 | 21 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 12 | 20 | 26 | 8 |
P value = 0.666 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 64 | 20 | 0.0 - 33.3 (3.2) |
subtype1 | 11 | 4 | 0.0 - 33.3 (0.3) |
subtype2 | 19 | 4 | 0.1 - 20.1 (0.2) |
subtype3 | 26 | 10 | 0.3 - 30.7 (6.8) |
subtype4 | 8 | 2 | 0.1 - 10.4 (0.1) |
P value = 0.0017 (Kruskal-Wallis (anova)), Q value = 0.082
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 66 | 62.1 (13.2) |
subtype1 | 12 | 58.8 (8.9) |
subtype2 | 20 | 56.6 (11.8) |
subtype3 | 26 | 69.0 (13.6) |
subtype4 | 8 | 58.1 (12.1) |
P value = 0.0228 (Fisher's exact test), Q value = 0.96
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 4 | 3 | 2 | 1 | 21 | 10 | 6 | 6 | 5 | 1 | 1 |
subtype1 | 0 | 1 | 0 | 0 | 4 | 1 | 3 | 2 | 1 | 0 | 0 |
subtype2 | 0 | 0 | 2 | 0 | 9 | 4 | 2 | 2 | 1 | 0 | 0 |
subtype3 | 4 | 2 | 0 | 0 | 2 | 5 | 0 | 2 | 3 | 1 | 1 |
subtype4 | 0 | 0 | 0 | 1 | 6 | 0 | 1 | 0 | 0 | 0 | 0 |
P value = 0.00688 (Fisher's exact test), Q value = 0.32
nPatients | T0+T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 9 | 16 | 36 |
subtype1 | 1 | 1 | 10 |
subtype2 | 0 | 7 | 13 |
subtype3 | 8 | 4 | 9 |
subtype4 | 0 | 4 | 4 |
P value = 0.251 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 35 | 18 | 7 | 1 |
subtype1 | 6 | 5 | 1 | 0 |
subtype2 | 14 | 5 | 1 | 0 |
subtype3 | 8 | 7 | 5 | 1 |
subtype4 | 7 | 1 | 0 | 0 |
P value = 0.127 (Fisher's exact test), Q value = 1
nPatients | M0 | M1A | MX |
---|---|---|---|
ALL | 49 | 1 | 7 |
subtype1 | 11 | 0 | 0 |
subtype2 | 18 | 0 | 2 |
subtype3 | 12 | 1 | 5 |
subtype4 | 8 | 0 | 0 |
P value = 0.138 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 10 | 56 |
subtype1 | 2 | 10 |
subtype2 | 1 | 19 |
subtype3 | 7 | 19 |
subtype4 | 0 | 8 |
P value = 0.675 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 41 | 36.8 (20.8) |
subtype1 | 8 | 44.3 (24.3) |
subtype2 | 12 | 36.7 (17.8) |
subtype3 | 17 | 34.2 (22.1) |
subtype4 | 4 | 33.8 (20.6) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00071
nPatients | ASIAN | WHITE |
---|---|---|
ALL | 27 | 36 |
subtype1 | 6 | 6 |
subtype2 | 14 | 6 |
subtype3 | 0 | 23 |
subtype4 | 7 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 60 | 54 | 10 |
P value = 0.413 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 116 | 37 | 0.0 - 122.1 (5.8) |
subtype1 | 60 | 21 | 0.3 - 122.1 (7.9) |
subtype2 | 47 | 13 | 0.0 - 53.9 (0.4) |
subtype3 | 9 | 3 | 0.3 - 83.2 (6.2) |
P value = 9.65e-06 (Kruskal-Wallis (anova)), Q value = 0.00069
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 124 | 63.8 (12.7) |
subtype1 | 60 | 68.0 (11.9) |
subtype2 | 54 | 57.8 (10.9) |
subtype3 | 10 | 70.2 (14.1) |
P value = 5e-05 (Fisher's exact test), Q value = 0.0031
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 | 33 | 22 | 16 | 8 | 6 | 4 | 2 | 1 |
subtype1 | 7 | 2 | 2 | 0 | 3 | 12 | 7 | 2 | 3 | 4 | 2 | 1 |
subtype2 | 0 | 1 | 2 | 1 | 27 | 9 | 8 | 3 | 3 | 0 | 0 | 0 |
subtype3 | 0 | 1 | 1 | 0 | 3 | 1 | 1 | 3 | 0 | 0 | 0 | 0 |
P value = 0.00142 (Fisher's exact test), Q value = 0.071
nPatients | T0+T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 21 | 30 | 62 |
subtype1 | 17 | 8 | 24 |
subtype2 | 3 | 20 | 31 |
subtype3 | 1 | 2 | 7 |
P value = 0.129 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 58 | 41 | 8 | 4 |
subtype1 | 19 | 21 | 5 | 4 |
subtype2 | 33 | 17 | 3 | 0 |
subtype3 | 6 | 3 | 0 | 0 |
P value = 0.0507 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | M1A | MX |
---|---|---|---|---|
ALL | 89 | 1 | 2 | 17 |
subtype1 | 32 | 1 | 2 | 11 |
subtype2 | 49 | 0 | 0 | 4 |
subtype3 | 8 | 0 | 0 | 2 |
P value = 0.587 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 18 | 106 |
subtype1 | 11 | 49 |
subtype2 | 6 | 48 |
subtype3 | 1 | 9 |
P value = 0.318 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 73 | 37.2 (21.3) |
subtype1 | 34 | 39.2 (24.1) |
subtype2 | 32 | 32.8 (15.4) |
subtype3 | 7 | 48.1 (27.4) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00071
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 35 | 1 | 83 |
subtype1 | 0 | 0 | 55 |
subtype2 | 34 | 1 | 19 |
subtype3 | 1 | 0 | 9 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 44 | 20 | 35 | 25 |
P value = 0.237 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 116 | 37 | 0.0 - 122.1 (5.8) |
subtype1 | 44 | 17 | 0.3 - 122.1 (7.3) |
subtype2 | 20 | 6 | 1.0 - 83.2 (8.7) |
subtype3 | 30 | 8 | 0.0 - 33.3 (0.3) |
subtype4 | 22 | 6 | 0.1 - 53.9 (1.0) |
P value = 0.000158 (Kruskal-Wallis (anova)), Q value = 0.0092
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 124 | 63.8 (12.7) |
subtype1 | 44 | 66.3 (12.7) |
subtype2 | 20 | 72.1 (10.5) |
subtype3 | 35 | 58.4 (12.8) |
subtype4 | 25 | 60.1 (9.9) |
P value = 0.0015 (Fisher's exact test), Q value = 0.073
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 | 33 | 22 | 16 | 8 | 6 | 4 | 2 | 1 |
subtype1 | 6 | 2 | 2 | 0 | 1 | 9 | 5 | 1 | 2 | 3 | 1 | 1 |
subtype2 | 1 | 0 | 0 | 0 | 4 | 4 | 2 | 2 | 1 | 1 | 1 | 0 |
subtype3 | 0 | 1 | 2 | 1 | 12 | 7 | 7 | 3 | 2 | 0 | 0 | 0 |
subtype4 | 0 | 1 | 1 | 0 | 16 | 2 | 2 | 2 | 1 | 0 | 0 | 0 |
P value = 0.00017 (Fisher's exact test), Q value = 0.0097
nPatients | T0+T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 21 | 30 | 62 |
subtype1 | 16 | 8 | 12 |
subtype2 | 1 | 2 | 14 |
subtype3 | 2 | 10 | 23 |
subtype4 | 2 | 10 | 13 |
P value = 0.184 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 58 | 41 | 8 | 4 |
subtype1 | 13 | 17 | 3 | 3 |
subtype2 | 8 | 5 | 2 | 1 |
subtype3 | 19 | 13 | 2 | 0 |
subtype4 | 18 | 6 | 1 | 0 |
P value = 0.0805 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | M1A | MX |
---|---|---|---|---|
ALL | 89 | 1 | 2 | 17 |
subtype1 | 22 | 1 | 1 | 9 |
subtype2 | 13 | 0 | 1 | 3 |
subtype3 | 31 | 0 | 0 | 4 |
subtype4 | 23 | 0 | 0 | 1 |
P value = 0.55 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 18 | 106 |
subtype1 | 8 | 36 |
subtype2 | 4 | 16 |
subtype3 | 3 | 32 |
subtype4 | 3 | 22 |
P value = 0.698 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 73 | 37.2 (21.3) |
subtype1 | 24 | 35.0 (18.5) |
subtype2 | 12 | 47.4 (31.6) |
subtype3 | 19 | 36.8 (20.1) |
subtype4 | 18 | 33.9 (17.0) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00071
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 35 | 1 | 83 |
subtype1 | 0 | 0 | 40 |
subtype2 | 0 | 0 | 19 |
subtype3 | 18 | 1 | 16 |
subtype4 | 17 | 0 | 8 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 56 | 50 | 18 |
P value = 0.455 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 116 | 37 | 0.0 - 122.1 (5.8) |
subtype1 | 56 | 21 | 0.3 - 122.1 (7.9) |
subtype2 | 43 | 12 | 0.0 - 53.9 (0.5) |
subtype3 | 17 | 4 | 0.1 - 83.2 (3.8) |
P value = 2.45e-05 (Kruskal-Wallis (anova)), Q value = 0.0015
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 124 | 63.8 (12.7) |
subtype1 | 56 | 67.9 (12.2) |
subtype2 | 50 | 57.6 (10.8) |
subtype3 | 18 | 68.1 (12.6) |
P value = 0.00066 (Fisher's exact test), Q value = 0.034
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 | 33 | 22 | 16 | 8 | 6 | 4 | 2 | 1 |
subtype1 | 7 | 2 | 2 | 0 | 3 | 10 | 7 | 2 | 2 | 3 | 2 | 1 |
subtype2 | 0 | 1 | 2 | 1 | 25 | 8 | 7 | 3 | 3 | 0 | 0 | 0 |
subtype3 | 0 | 1 | 1 | 0 | 5 | 4 | 2 | 3 | 1 | 1 | 0 | 0 |
P value = 0.00092 (Fisher's exact test), Q value = 0.047
nPatients | T0+T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 21 | 30 | 62 |
subtype1 | 17 | 8 | 20 |
subtype2 | 3 | 17 | 30 |
subtype3 | 1 | 5 | 12 |
P value = 0.135 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 58 | 41 | 8 | 4 |
subtype1 | 17 | 21 | 4 | 3 |
subtype2 | 31 | 15 | 3 | 0 |
subtype3 | 10 | 5 | 1 | 1 |
P value = 0.0354 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | M1A | MX |
---|---|---|---|---|
ALL | 89 | 1 | 2 | 17 |
subtype1 | 28 | 1 | 2 | 11 |
subtype2 | 45 | 0 | 0 | 4 |
subtype3 | 16 | 0 | 0 | 2 |
P value = 0.3 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 18 | 106 |
subtype1 | 11 | 45 |
subtype2 | 6 | 44 |
subtype3 | 1 | 17 |
P value = 0.132 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 73 | 37.2 (21.3) |
subtype1 | 30 | 38.3 (22.5) |
subtype2 | 30 | 31.6 (14.9) |
subtype3 | 13 | 47.7 (27.4) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00071
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 35 | 1 | 83 |
subtype1 | 0 | 0 | 51 |
subtype2 | 31 | 1 | 18 |
subtype3 | 4 | 0 | 14 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 48 | 15 | 61 |
P value = 0.16 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 116 | 37 | 0.0 - 122.1 (5.8) |
subtype1 | 48 | 20 | 0.3 - 122.1 (7.3) |
subtype2 | 15 | 3 | 1.0 - 83.2 (13.2) |
subtype3 | 53 | 14 | 0.0 - 53.9 (0.5) |
P value = 0.000356 (Kruskal-Wallis (anova)), Q value = 0.019
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 124 | 63.8 (12.7) |
subtype1 | 48 | 66.8 (12.5) |
subtype2 | 15 | 71.1 (10.6) |
subtype3 | 61 | 59.6 (12.0) |
P value = 5e-05 (Fisher's exact test), Q value = 0.0031
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 | 33 | 22 | 16 | 8 | 6 | 4 | 2 | 1 |
subtype1 | 6 | 2 | 2 | 0 | 1 | 9 | 5 | 1 | 2 | 3 | 2 | 1 |
subtype2 | 1 | 0 | 0 | 0 | 4 | 3 | 2 | 2 | 1 | 1 | 0 | 0 |
subtype3 | 0 | 2 | 3 | 1 | 28 | 10 | 9 | 5 | 3 | 0 | 0 | 0 |
P value = 6e-05 (Fisher's exact test), Q value = 0.0036
nPatients | T0+T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 21 | 30 | 62 |
subtype1 | 16 | 8 | 13 |
subtype2 | 1 | 1 | 13 |
subtype3 | 4 | 21 | 36 |
P value = 0.0261 (Fisher's exact test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 58 | 41 | 8 | 4 |
subtype1 | 13 | 18 | 3 | 3 |
subtype2 | 8 | 3 | 2 | 1 |
subtype3 | 37 | 20 | 3 | 0 |
P value = 0.0131 (Fisher's exact test), Q value = 0.6
nPatients | M0 | M1 | M1A | MX |
---|---|---|---|---|
ALL | 89 | 1 | 2 | 17 |
subtype1 | 22 | 1 | 2 | 9 |
subtype2 | 12 | 0 | 0 | 3 |
subtype3 | 55 | 0 | 0 | 5 |
P value = 0.322 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 18 | 106 |
subtype1 | 9 | 39 |
subtype2 | 3 | 12 |
subtype3 | 6 | 55 |
P value = 0.251 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 73 | 37.2 (21.3) |
subtype1 | 27 | 35.8 (20.0) |
subtype2 | 8 | 53.2 (32.2) |
subtype3 | 38 | 34.9 (18.4) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00071
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 35 | 1 | 83 |
subtype1 | 0 | 0 | 44 |
subtype2 | 0 | 0 | 14 |
subtype3 | 35 | 1 | 25 |
-
Cluster data file = ESCA-TP.mergedcluster.txt
-
Clinical data file = ESCA-TP.merged_data.txt
-
Number of patients = 127
-
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.