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 124 patients, 29 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 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.
-
4 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'Time to Death', 'YEARS_TO_BIRTH', and 'HISTOLOGICAL_TYPE'.
-
CNMF clustering analysis on RPPA data identified 3 subtypes that correlate to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.
-
Consensus hierarchical clustering analysis on RPPA data identified 4 subtypes that correlate to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
-
CNMF clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that correlate to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
-
Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that correlate to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
-
2 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
-
6 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes correlate to 'Time to Death', 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
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3 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes correlate to 'Time to Death', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
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4 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes correlate to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
TUMOR TISSUE SITE |
GENDER |
RADIATION THERAPY |
HISTOLOGICAL TYPE |
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 |
0.114 (0.227) |
0.00975 (0.0349) |
0.0605 (0.151) |
0.788 (0.9) |
0.0911 (0.203) |
5e-05 (0.000364) |
0.668 (0.81) |
0.158 (0.286) |
METHLYATION CNMF |
0.01 (0.0349) |
0.00205 (0.00963) |
0.111 (0.227) |
0.668 (0.81) |
0.29 (0.429) |
1e-05 (8.89e-05) |
0.187 (0.326) |
0.255 (0.418) |
RPPA CNMF subtypes |
0.434 (0.569) |
4.97e-05 (0.000364) |
0.58 (0.74) |
0.323 (0.461) |
0.427 (0.569) |
1e-05 (8.89e-05) |
0.263 (0.418) |
0.583 (0.74) |
RPPA cHierClus subtypes |
0.0913 (0.203) |
0.00733 (0.0309) |
0.933 (0.974) |
0.748 (0.88) |
0.0456 (0.126) |
1e-05 (8.89e-05) |
0.779 (0.9) |
0.266 (0.418) |
RNAseq CNMF subtypes |
0.105 (0.227) |
0.00984 (0.0349) |
0.938 (0.974) |
0.303 (0.441) |
0.0144 (0.0461) |
1e-05 (8.89e-05) |
0.91 (0.973) |
0.127 (0.247) |
RNAseq cHierClus subtypes |
0.267 (0.418) |
0.0033 (0.0147) |
0.973 (0.998) |
0.818 (0.916) |
0.00163 (0.00815) |
1e-05 (8.89e-05) |
0.414 (0.569) |
0.275 (0.419) |
MIRSEQ CNMF |
0.0792 (0.192) |
0.0113 (0.0376) |
0.278 (0.419) |
1 (1.00) |
8.67e-05 (0.000554) |
1e-05 (8.89e-05) |
1 (1.00) |
0.0522 (0.135) |
MIRSEQ CHIERARCHICAL |
0.0189 (0.055) |
0.00796 (0.0318) |
0.387 (0.543) |
0.163 (0.29) |
0.00062 (0.00331) |
1e-05 (8.89e-05) |
0.825 (0.916) |
0.139 (0.265) |
MIRseq Mature CNMF subtypes |
0.0158 (0.0485) |
0.0866 (0.203) |
0.697 (0.832) |
0.911 (0.973) |
9e-05 (0.000554) |
1e-05 (8.89e-05) |
0.626 (0.783) |
0.108 (0.227) |
MIRseq Mature cHierClus subtypes |
0.147 (0.274) |
0.0193 (0.055) |
0.421 (0.569) |
0.0509 (0.135) |
0.00029 (0.00166) |
1e-05 (8.89e-05) |
0.912 (0.973) |
0.209 (0.355) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 65 | 31 | 27 |
P value = 0.114 (logrank test), Q value = 0.23
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 122 | 9 | 0.5 - 150.0 (40.6) |
subtype1 | 65 | 2 | 0.5 - 150.0 (37.6) |
subtype2 | 31 | 5 | 1.6 - 123.7 (49.8) |
subtype3 | 26 | 2 | 4.1 - 120.4 (45.8) |
P value = 0.00975 (Kruskal-Wallis (anova)), Q value = 0.035
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 122 | 58.3 (13.0) |
subtype1 | 65 | 58.4 (11.7) |
subtype2 | 31 | 53.0 (15.1) |
subtype3 | 26 | 64.1 (11.4) |
P value = 0.0605 (Fisher's exact test), Q value = 0.15
nPatients | ANTERIOR MEDIASTINUM | THYMUS |
---|---|---|
ALL | 27 | 96 |
subtype1 | 9 | 56 |
subtype2 | 10 | 21 |
subtype3 | 8 | 19 |
P value = 0.788 (Fisher's exact test), Q value = 0.9
nPatients | FEMALE | MALE |
---|---|---|
ALL | 59 | 64 |
subtype1 | 29 | 36 |
subtype2 | 16 | 15 |
subtype3 | 14 | 13 |
P value = 0.0911 (Fisher's exact test), Q value = 0.2
nPatients | NO | YES |
---|---|---|
ALL | 81 | 42 |
subtype1 | 48 | 17 |
subtype2 | 16 | 15 |
subtype3 | 17 | 10 |
P value = 5e-05 (Fisher's exact test), Q value = 0.00036
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
subtype1 | 10 | 24 | 13 | 11 | 2 | 5 |
subtype2 | 0 | 4 | 1 | 15 | 7 | 4 |
subtype3 | 7 | 10 | 1 | 4 | 3 | 2 |
P value = 0.668 (Fisher's exact test), Q value = 0.81
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 13 | 6 | 102 |
subtype1 | 6 | 4 | 54 |
subtype2 | 4 | 0 | 26 |
subtype3 | 3 | 2 | 22 |
P value = 0.158 (Fisher's exact test), Q value = 0.29
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 9 | 100 |
subtype1 | 2 | 54 |
subtype2 | 4 | 23 |
subtype3 | 3 | 23 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 39 | 36 | 25 | 24 |
P value = 0.01 (logrank test), Q value = 0.035
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 123 | 9 | 0.5 - 150.0 (41.2) |
subtype1 | 39 | 0 | 10.7 - 138.9 (50.8) |
subtype2 | 36 | 4 | 1.6 - 120.4 (36.9) |
subtype3 | 25 | 5 | 5.9 - 133.8 (48.9) |
subtype4 | 23 | 0 | 0.5 - 150.0 (35.2) |
P value = 0.00205 (Kruskal-Wallis (anova)), Q value = 0.0096
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 123 | 58.2 (13.0) |
subtype1 | 39 | 54.2 (12.5) |
subtype2 | 36 | 64.9 (10.5) |
subtype3 | 25 | 54.5 (14.2) |
subtype4 | 23 | 58.3 (12.4) |
P value = 0.111 (Fisher's exact test), Q value = 0.23
nPatients | ANTERIOR MEDIASTINUM | THYMUS |
---|---|---|
ALL | 27 | 97 |
subtype1 | 5 | 34 |
subtype2 | 6 | 30 |
subtype3 | 9 | 16 |
subtype4 | 7 | 17 |
P value = 0.668 (Fisher's exact test), Q value = 0.81
nPatients | FEMALE | MALE |
---|---|---|
ALL | 60 | 64 |
subtype1 | 18 | 21 |
subtype2 | 15 | 21 |
subtype3 | 14 | 11 |
subtype4 | 13 | 11 |
P value = 0.29 (Fisher's exact test), Q value = 0.43
nPatients | NO | YES |
---|---|---|
ALL | 81 | 43 |
subtype1 | 24 | 15 |
subtype2 | 26 | 10 |
subtype3 | 13 | 12 |
subtype4 | 18 | 6 |
P value = 1e-05 (Fisher's exact test), Q value = 8.9e-05
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 31 | 12 | 11 |
subtype1 | 0 | 7 | 14 | 15 | 3 | 0 |
subtype2 | 14 | 11 | 0 | 0 | 3 | 8 |
subtype3 | 2 | 2 | 1 | 11 | 6 | 3 |
subtype4 | 1 | 18 | 0 | 5 | 0 | 0 |
P value = 0.187 (Fisher's exact test), Q value = 0.33
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 13 | 6 | 103 |
subtype1 | 2 | 5 | 32 |
subtype2 | 5 | 1 | 30 |
subtype3 | 2 | 0 | 22 |
subtype4 | 4 | 0 | 19 |
P value = 0.255 (Fisher's exact test), Q value = 0.42
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 10 | 100 |
subtype1 | 1 | 34 |
subtype2 | 3 | 30 |
subtype3 | 4 | 18 |
subtype4 | 2 | 18 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 31 | 25 | 34 |
P value = 0.434 (logrank test), Q value = 0.57
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 89 | 8 | 1.6 - 150.0 (34.6) |
subtype1 | 30 | 4 | 1.6 - 150.0 (33.5) |
subtype2 | 25 | 2 | 4.1 - 97.4 (38.3) |
subtype3 | 34 | 2 | 2.4 - 138.9 (32.9) |
P value = 4.97e-05 (Kruskal-Wallis (anova)), Q value = 0.00036
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 89 | 58.1 (12.9) |
subtype1 | 30 | 57.2 (14.3) |
subtype2 | 25 | 67.0 (9.0) |
subtype3 | 34 | 52.4 (10.5) |
P value = 0.58 (Fisher's exact test), Q value = 0.74
nPatients | ANTERIOR MEDIASTINUM | THYMUS |
---|---|---|
ALL | 22 | 68 |
subtype1 | 6 | 25 |
subtype2 | 8 | 17 |
subtype3 | 8 | 26 |
P value = 0.323 (Fisher's exact test), Q value = 0.46
nPatients | FEMALE | MALE |
---|---|---|
ALL | 43 | 47 |
subtype1 | 14 | 17 |
subtype2 | 15 | 10 |
subtype3 | 14 | 20 |
P value = 0.427 (Fisher's exact test), Q value = 0.57
nPatients | NO | YES |
---|---|---|
ALL | 62 | 28 |
subtype1 | 19 | 12 |
subtype2 | 17 | 8 |
subtype3 | 26 | 8 |
P value = 1e-05 (Fisher's exact test), Q value = 8.9e-05
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 11 | 28 | 12 | 24 | 5 | 10 |
subtype1 | 4 | 5 | 1 | 10 | 4 | 7 |
subtype2 | 7 | 14 | 0 | 1 | 1 | 2 |
subtype3 | 0 | 9 | 11 | 13 | 0 | 1 |
P value = 0.263 (Fisher's exact test), Q value = 0.42
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 11 | 4 | 73 |
subtype1 | 6 | 0 | 24 |
subtype2 | 3 | 1 | 21 |
subtype3 | 2 | 3 | 28 |
P value = 0.583 (Fisher's exact test), Q value = 0.74
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 72 |
subtype1 | 4 | 23 |
subtype2 | 2 | 20 |
subtype3 | 2 | 29 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 16 | 23 | 31 | 20 |
P value = 0.0913 (logrank test), Q value = 0.2
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 89 | 8 | 1.6 - 150.0 (34.6) |
subtype1 | 16 | 1 | 13.9 - 107.4 (30.3) |
subtype2 | 22 | 2 | 4.1 - 95.7 (35.3) |
subtype3 | 31 | 1 | 2.4 - 150.0 (49.2) |
subtype4 | 20 | 4 | 1.6 - 120.4 (27.7) |
P value = 0.00733 (Kruskal-Wallis (anova)), Q value = 0.031
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 89 | 58.1 (12.9) |
subtype1 | 16 | 57.9 (9.8) |
subtype2 | 22 | 65.3 (11.1) |
subtype3 | 31 | 53.1 (11.8) |
subtype4 | 20 | 58.1 (15.4) |
P value = 0.933 (Fisher's exact test), Q value = 0.97
nPatients | ANTERIOR MEDIASTINUM | THYMUS |
---|---|---|
ALL | 22 | 68 |
subtype1 | 5 | 11 |
subtype2 | 5 | 18 |
subtype3 | 7 | 24 |
subtype4 | 5 | 15 |
P value = 0.748 (Fisher's exact test), Q value = 0.88
nPatients | FEMALE | MALE |
---|---|---|
ALL | 43 | 47 |
subtype1 | 7 | 9 |
subtype2 | 13 | 10 |
subtype3 | 13 | 18 |
subtype4 | 10 | 10 |
P value = 0.0456 (Fisher's exact test), Q value = 0.13
nPatients | NO | YES |
---|---|---|
ALL | 62 | 28 |
subtype1 | 13 | 3 |
subtype2 | 19 | 4 |
subtype3 | 21 | 10 |
subtype4 | 9 | 11 |
P value = 1e-05 (Fisher's exact test), Q value = 8.9e-05
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 11 | 28 | 12 | 24 | 5 | 10 |
subtype1 | 0 | 9 | 2 | 5 | 0 | 0 |
subtype2 | 10 | 9 | 0 | 2 | 1 | 1 |
subtype3 | 0 | 9 | 10 | 12 | 0 | 0 |
subtype4 | 1 | 1 | 0 | 5 | 4 | 9 |
P value = 0.779 (Fisher's exact test), Q value = 0.9
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 11 | 4 | 73 |
subtype1 | 2 | 1 | 13 |
subtype2 | 3 | 1 | 19 |
subtype3 | 2 | 2 | 26 |
subtype4 | 4 | 0 | 15 |
P value = 0.266 (Fisher's exact test), Q value = 0.42
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 72 |
subtype1 | 1 | 13 |
subtype2 | 1 | 20 |
subtype3 | 2 | 26 |
subtype4 | 4 | 13 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 46 | 31 | 29 | 14 |
P value = 0.105 (logrank test), Q value = 0.23
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 119 | 9 | 0.5 - 150.0 (40.1) |
subtype1 | 46 | 5 | 1.6 - 138.5 (50.3) |
subtype2 | 31 | 0 | 2.4 - 150.0 (38.3) |
subtype3 | 28 | 2 | 0.5 - 120.4 (41.7) |
subtype4 | 14 | 2 | 11.6 - 58.8 (29.3) |
P value = 0.00984 (Kruskal-Wallis (anova)), Q value = 0.035
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 119 | 57.9 (13.1) |
subtype1 | 46 | 53.1 (14.3) |
subtype2 | 31 | 58.2 (10.7) |
subtype3 | 28 | 63.8 (11.9) |
subtype4 | 14 | 61.1 (10.6) |
P value = 0.938 (Fisher's exact test), Q value = 0.97
nPatients | ANTERIOR MEDIASTINUM | THYMUS |
---|---|---|
ALL | 27 | 93 |
subtype1 | 12 | 34 |
subtype2 | 6 | 25 |
subtype3 | 6 | 23 |
subtype4 | 3 | 11 |
P value = 0.303 (Fisher's exact test), Q value = 0.44
nPatients | FEMALE | MALE |
---|---|---|
ALL | 57 | 63 |
subtype1 | 20 | 26 |
subtype2 | 14 | 17 |
subtype3 | 13 | 16 |
subtype4 | 10 | 4 |
P value = 0.0144 (Fisher's exact test), Q value = 0.046
nPatients | NO | YES |
---|---|---|
ALL | 78 | 42 |
subtype1 | 24 | 22 |
subtype2 | 26 | 5 |
subtype3 | 21 | 8 |
subtype4 | 7 | 7 |
P value = 1e-05 (Fisher's exact test), Q value = 8.9e-05
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 35 | 15 | 31 | 11 | 11 |
subtype1 | 1 | 3 | 12 | 23 | 7 | 0 |
subtype2 | 5 | 16 | 3 | 7 | 0 | 0 |
subtype3 | 10 | 16 | 0 | 0 | 1 | 2 |
subtype4 | 1 | 0 | 0 | 1 | 3 | 9 |
P value = 0.91 (Fisher's exact test), Q value = 0.97
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 12 | 6 | 100 |
subtype1 | 3 | 3 | 39 |
subtype2 | 3 | 2 | 25 |
subtype3 | 4 | 1 | 24 |
subtype4 | 2 | 0 | 12 |
P value = 0.127 (Fisher's exact test), Q value = 0.25
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 10 | 96 |
subtype1 | 4 | 35 |
subtype2 | 3 | 25 |
subtype3 | 0 | 25 |
subtype4 | 3 | 11 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 48 | 42 | 20 | 10 |
P value = 0.267 (logrank test), Q value = 0.42
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 119 | 9 | 0.5 - 150.0 (40.1) |
subtype1 | 48 | 5 | 1.6 - 138.5 (50.2) |
subtype2 | 41 | 1 | 0.5 - 150.0 (36.6) |
subtype3 | 20 | 1 | 12.7 - 112.1 (47.0) |
subtype4 | 10 | 2 | 11.6 - 120.4 (27.7) |
P value = 0.0033 (Kruskal-Wallis (anova)), Q value = 0.015
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 119 | 57.9 (13.1) |
subtype1 | 48 | 53.0 (14.2) |
subtype2 | 41 | 58.6 (10.5) |
subtype3 | 20 | 65.4 (11.7) |
subtype4 | 10 | 63.1 (11.0) |
P value = 0.973 (Fisher's exact test), Q value = 1
nPatients | ANTERIOR MEDIASTINUM | THYMUS |
---|---|---|
ALL | 27 | 93 |
subtype1 | 12 | 36 |
subtype2 | 9 | 33 |
subtype3 | 4 | 16 |
subtype4 | 2 | 8 |
P value = 0.818 (Fisher's exact test), Q value = 0.92
nPatients | FEMALE | MALE |
---|---|---|
ALL | 57 | 63 |
subtype1 | 21 | 27 |
subtype2 | 20 | 22 |
subtype3 | 10 | 10 |
subtype4 | 6 | 4 |
P value = 0.00163 (Fisher's exact test), Q value = 0.0081
nPatients | NO | YES |
---|---|---|
ALL | 78 | 42 |
subtype1 | 24 | 24 |
subtype2 | 35 | 7 |
subtype3 | 15 | 5 |
subtype4 | 4 | 6 |
P value = 1e-05 (Fisher's exact test), Q value = 8.9e-05
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 35 | 15 | 31 | 11 | 11 |
subtype1 | 1 | 3 | 12 | 23 | 9 | 0 |
subtype2 | 5 | 28 | 3 | 6 | 0 | 0 |
subtype3 | 11 | 4 | 0 | 2 | 2 | 1 |
subtype4 | 0 | 0 | 0 | 0 | 0 | 10 |
P value = 0.414 (Fisher's exact test), Q value = 0.57
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 12 | 6 | 100 |
subtype1 | 3 | 3 | 41 |
subtype2 | 4 | 3 | 34 |
subtype3 | 2 | 0 | 18 |
subtype4 | 3 | 0 | 7 |
P value = 0.275 (Fisher's exact test), Q value = 0.42
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 10 | 96 |
subtype1 | 5 | 36 |
subtype2 | 3 | 34 |
subtype3 | 0 | 18 |
subtype4 | 2 | 8 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 59 | 61 | 1 | 2 | 1 |
P value = 0.0792 (logrank test), Q value = 0.19
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 119 | 7 | 0.5 - 150.0 (40.1) |
subtype1 | 59 | 6 | 1.6 - 138.5 (48.7) |
subtype2 | 60 | 1 | 0.5 - 150.0 (39.2) |
P value = 0.0113 (Wilcoxon-test), Q value = 0.038
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 119 | 57.8 (13.0) |
subtype1 | 59 | 54.5 (14.0) |
subtype2 | 60 | 61.1 (11.2) |
P value = 0.278 (Fisher's exact test), Q value = 0.42
nPatients | ANTERIOR MEDIASTINUM | THYMUS |
---|---|---|
ALL | 27 | 93 |
subtype1 | 16 | 43 |
subtype2 | 11 | 50 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 58 | 62 |
subtype1 | 29 | 30 |
subtype2 | 29 | 32 |
P value = 8.67e-05 (Fisher's exact test), Q value = 0.00055
nPatients | NO | YES |
---|---|---|
ALL | 80 | 40 |
subtype1 | 29 | 30 |
subtype2 | 51 | 10 |
P value = 1e-05 (Fisher's exact test), Q value = 8.9e-05
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 16 | 37 | 14 | 31 | 11 | 11 |
subtype1 | 2 | 5 | 11 | 23 | 8 | 10 |
subtype2 | 14 | 32 | 3 | 8 | 3 | 1 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 13 | 6 | 99 |
subtype1 | 6 | 3 | 49 |
subtype2 | 7 | 3 | 50 |
P value = 0.0522 (Fisher's exact test), Q value = 0.13
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 10 | 97 |
subtype1 | 8 | 45 |
subtype2 | 2 | 52 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 27 | 18 | 29 | 7 | 16 | 27 |
P value = 0.0189 (logrank test), Q value = 0.055
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 123 | 9 | 0.5 - 150.0 (41.2) |
subtype1 | 27 | 3 | 12.7 - 123.7 (52.9) |
subtype2 | 17 | 1 | 0.5 - 150.0 (34.6) |
subtype3 | 29 | 3 | 1.6 - 138.5 (37.6) |
subtype4 | 7 | 2 | 11.6 - 58.8 (28.0) |
subtype5 | 16 | 0 | 12.7 - 112.1 (43.8) |
subtype6 | 27 | 0 | 2.4 - 138.9 (38.3) |
P value = 0.00796 (Kruskal-Wallis (anova)), Q value = 0.032
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 123 | 58.2 (13.0) |
subtype1 | 27 | 51.2 (14.0) |
subtype2 | 17 | 58.4 (10.4) |
subtype3 | 29 | 57.5 (13.8) |
subtype4 | 7 | 62.6 (11.4) |
subtype5 | 16 | 67.8 (8.3) |
subtype6 | 27 | 58.9 (11.9) |
P value = 0.387 (Fisher's exact test), Q value = 0.54
nPatients | ANTERIOR MEDIASTINUM | THYMUS |
---|---|---|
ALL | 27 | 97 |
subtype1 | 4 | 23 |
subtype2 | 3 | 15 |
subtype3 | 11 | 18 |
subtype4 | 1 | 6 |
subtype5 | 3 | 13 |
subtype6 | 5 | 22 |
P value = 0.163 (Fisher's exact test), Q value = 0.29
nPatients | FEMALE | MALE |
---|---|---|
ALL | 60 | 64 |
subtype1 | 8 | 19 |
subtype2 | 8 | 10 |
subtype3 | 19 | 10 |
subtype4 | 4 | 3 |
subtype5 | 7 | 9 |
subtype6 | 14 | 13 |
P value = 0.00062 (Fisher's exact test), Q value = 0.0033
nPatients | NO | YES |
---|---|---|
ALL | 81 | 43 |
subtype1 | 12 | 15 |
subtype2 | 14 | 4 |
subtype3 | 15 | 14 |
subtype4 | 3 | 4 |
subtype5 | 12 | 4 |
subtype6 | 25 | 2 |
P value = 1e-05 (Fisher's exact test), Q value = 8.9e-05
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 31 | 12 | 11 |
subtype1 | 0 | 4 | 3 | 15 | 4 | 1 |
subtype2 | 4 | 13 | 0 | 1 | 0 | 0 |
subtype3 | 3 | 2 | 9 | 8 | 5 | 2 |
subtype4 | 0 | 0 | 0 | 0 | 0 | 7 |
subtype5 | 8 | 3 | 0 | 1 | 3 | 1 |
subtype6 | 2 | 16 | 3 | 6 | 0 | 0 |
P value = 0.825 (Fisher's exact test), Q value = 0.92
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 13 | 6 | 103 |
subtype1 | 3 | 1 | 22 |
subtype2 | 2 | 1 | 15 |
subtype3 | 1 | 2 | 26 |
subtype4 | 2 | 0 | 5 |
subtype5 | 2 | 0 | 14 |
subtype6 | 3 | 2 | 21 |
P value = 0.139 (Fisher's exact test), Q value = 0.27
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 10 | 100 |
subtype1 | 1 | 20 |
subtype2 | 1 | 14 |
subtype3 | 5 | 23 |
subtype4 | 2 | 5 |
subtype5 | 0 | 14 |
subtype6 | 1 | 24 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 18 | 59 | 47 |
P value = 0.0158 (logrank test), Q value = 0.048
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 123 | 9 | 0.5 - 150.0 (41.2) |
subtype1 | 18 | 0 | 10.7 - 138.5 (44.6) |
subtype2 | 58 | 1 | 0.5 - 150.0 (39.2) |
subtype3 | 47 | 8 | 1.6 - 133.8 (48.9) |
P value = 0.0866 (Kruskal-Wallis (anova)), Q value = 0.2
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 123 | 58.2 (13.0) |
subtype1 | 18 | 54.2 (13.9) |
subtype2 | 58 | 61.1 (11.4) |
subtype3 | 47 | 56.1 (14.0) |
P value = 0.697 (Fisher's exact test), Q value = 0.83
nPatients | ANTERIOR MEDIASTINUM | THYMUS |
---|---|---|
ALL | 27 | 97 |
subtype1 | 4 | 14 |
subtype2 | 11 | 48 |
subtype3 | 12 | 35 |
P value = 0.911 (Fisher's exact test), Q value = 0.97
nPatients | FEMALE | MALE |
---|---|---|
ALL | 60 | 64 |
subtype1 | 8 | 10 |
subtype2 | 28 | 31 |
subtype3 | 24 | 23 |
P value = 9e-05 (Fisher's exact test), Q value = 0.00055
nPatients | NO | YES |
---|---|---|
ALL | 81 | 43 |
subtype1 | 10 | 8 |
subtype2 | 50 | 9 |
subtype3 | 21 | 26 |
P value = 1e-05 (Fisher's exact test), Q value = 8.9e-05
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 31 | 12 | 11 |
subtype1 | 0 | 1 | 10 | 5 | 2 | 0 |
subtype2 | 14 | 32 | 3 | 7 | 2 | 1 |
subtype3 | 3 | 5 | 2 | 19 | 8 | 10 |
P value = 0.626 (Fisher's exact test), Q value = 0.78
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 13 | 6 | 103 |
subtype1 | 1 | 2 | 15 |
subtype2 | 7 | 3 | 48 |
subtype3 | 5 | 1 | 40 |
P value = 0.108 (Fisher's exact test), Q value = 0.23
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 10 | 100 |
subtype1 | 1 | 14 |
subtype2 | 2 | 50 |
subtype3 | 7 | 36 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 29 | 33 | 34 | 28 |
P value = 0.147 (logrank test), Q value = 0.27
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 123 | 9 | 0.5 - 150.0 (41.2) |
subtype1 | 29 | 3 | 10.4 - 123.7 (52.8) |
subtype2 | 32 | 1 | 0.5 - 112.1 (36.9) |
subtype3 | 34 | 5 | 1.6 - 138.5 (32.6) |
subtype4 | 28 | 0 | 2.4 - 150.0 (43.0) |
P value = 0.0193 (Kruskal-Wallis (anova)), Q value = 0.055
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 123 | 58.2 (13.0) |
subtype1 | 29 | 52.1 (14.0) |
subtype2 | 32 | 63.3 (10.4) |
subtype3 | 34 | 58.1 (13.7) |
subtype4 | 28 | 58.6 (11.7) |
P value = 0.421 (Fisher's exact test), Q value = 0.57
nPatients | ANTERIOR MEDIASTINUM | THYMUS |
---|---|---|
ALL | 27 | 97 |
subtype1 | 5 | 24 |
subtype2 | 6 | 27 |
subtype3 | 11 | 23 |
subtype4 | 5 | 23 |
P value = 0.0509 (Fisher's exact test), Q value = 0.13
nPatients | FEMALE | MALE |
---|---|---|
ALL | 60 | 64 |
subtype1 | 9 | 20 |
subtype2 | 14 | 19 |
subtype3 | 22 | 12 |
subtype4 | 15 | 13 |
P value = 0.00029 (Fisher's exact test), Q value = 0.0017
nPatients | NO | YES |
---|---|---|
ALL | 81 | 43 |
subtype1 | 13 | 16 |
subtype2 | 27 | 6 |
subtype3 | 17 | 17 |
subtype4 | 24 | 4 |
P value = 1e-05 (Fisher's exact test), Q value = 8.9e-05
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 31 | 12 | 11 |
subtype1 | 0 | 4 | 3 | 15 | 5 | 2 |
subtype2 | 12 | 16 | 0 | 1 | 3 | 1 |
subtype3 | 3 | 2 | 9 | 8 | 4 | 8 |
subtype4 | 2 | 16 | 3 | 7 | 0 | 0 |
P value = 0.912 (Fisher's exact test), Q value = 0.97
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 13 | 6 | 103 |
subtype1 | 4 | 1 | 23 |
subtype2 | 4 | 1 | 28 |
subtype3 | 2 | 2 | 30 |
subtype4 | 3 | 2 | 22 |
P value = 0.209 (Fisher's exact test), Q value = 0.36
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 10 | 100 |
subtype1 | 2 | 21 |
subtype2 | 1 | 28 |
subtype3 | 6 | 27 |
subtype4 | 1 | 24 |
-
Cluster data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THYM-TP/20140903/THYM-TP.mergedcluster.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/THYM-TP/19775615/THYM-TP.merged_data.txt
-
Number of patients = 124
-
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.