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, 35 significant findings detected with P value < 0.05 and Q value < 0.25.
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5 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes correlate to 'YEARS_TO_BIRTH', 'GENDER', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
-
7 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'Time to Death', 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
-
CNMF clustering analysis on RPPA data identified 3 subtypes that correlate to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.
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Consensus hierarchical clustering analysis on RPPA data identified 4 subtypes that correlate to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that correlate to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that correlate to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
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3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'Time to Death', 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
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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', 'YEARS_TO_BIRTH', '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', 'GENDER', '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 |
0.443 (0.591) |
0.000118 (0.000725) |
0.374 (0.554) |
0.0494 (0.113) |
0.0319 (0.0851) |
1e-05 (7.27e-05) |
0.424 (0.58) |
0.697 (0.833) |
METHLYATION CNMF |
0.0285 (0.0785) |
0.00163 (0.00767) |
0.604 (0.744) |
0.914 (0.974) |
0.0477 (0.112) |
1e-05 (7.27e-05) |
0.534 (0.701) |
0.0588 (0.131) |
RPPA CNMF subtypes |
0.424 (0.58) |
4.97e-05 (0.000331) |
0.583 (0.729) |
0.32 (0.484) |
0.427 (0.58) |
1e-05 (7.27e-05) |
0.265 (0.439) |
0.58 (0.729) |
RPPA cHierClus subtypes |
0.0888 (0.187) |
0.00733 (0.0293) |
0.935 (0.974) |
0.749 (0.882) |
0.0464 (0.112) |
1e-05 (7.27e-05) |
0.778 (0.899) |
0.265 (0.439) |
RNAseq CNMF subtypes |
0.109 (0.212) |
0.0186 (0.0573) |
0.937 (0.974) |
0.309 (0.476) |
0.0158 (0.0527) |
1e-05 (7.27e-05) |
0.911 (0.974) |
0.114 (0.218) |
RNAseq cHierClus subtypes |
0.269 (0.439) |
0.0033 (0.0139) |
0.973 (0.986) |
0.821 (0.913) |
0.00173 (0.00769) |
1e-05 (7.27e-05) |
0.411 (0.58) |
0.275 (0.439) |
MIRSEQ CNMF |
0.00857 (0.0303) |
0.0475 (0.112) |
0.561 (0.724) |
0.952 (0.976) |
1e-05 (7.27e-05) |
1e-05 (7.27e-05) |
1 (1.00) |
0.119 (0.222) |
MIRSEQ CHIERARCHICAL |
0.0208 (0.0593) |
0.00796 (0.0303) |
0.387 (0.562) |
0.164 (0.285) |
0.00054 (0.0027) |
1e-05 (7.27e-05) |
0.822 (0.913) |
0.138 (0.251) |
MIRseq Mature CNMF subtypes |
0.0183 (0.0573) |
0.00872 (0.0303) |
0.786 (0.899) |
0.641 (0.777) |
0.0003 (0.00171) |
1e-05 (7.27e-05) |
0.0747 (0.162) |
0.0916 (0.188) |
MIRseq Mature cHierClus subtypes |
0.155 (0.275) |
0.0197 (0.0583) |
0.296 (0.465) |
0.0475 (0.112) |
0.00045 (0.0024) |
1e-05 (7.27e-05) |
0.881 (0.965) |
0.0967 (0.193) |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 36 | 27 | 19 | 31 | 10 |
P value = 0.443 (logrank test), Q value = 0.59
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 122 | 9 | 0.5 - 150.4 (40.6) |
subtype1 | 36 | 4 | 1.6 - 150.4 (49.2) |
subtype2 | 27 | 0 | 0.5 - 93.7 (37.8) |
subtype3 | 18 | 1 | 14.3 - 120.4 (41.3) |
subtype4 | 31 | 2 | 1.9 - 138.9 (42.1) |
subtype5 | 10 | 2 | 5.9 - 150.0 (36.4) |
P value = 0.000118 (Kruskal-Wallis (anova)), Q value = 0.00073
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 122 | 58.3 (13.0) |
subtype1 | 36 | 49.8 (13.2) |
subtype2 | 27 | 62.6 (10.9) |
subtype3 | 18 | 65.7 (8.2) |
subtype4 | 31 | 59.9 (10.8) |
subtype5 | 10 | 58.6 (16.3) |
P value = 0.374 (Fisher's exact test), Q value = 0.55
nPatients | ANTERIOR MEDIASTINUM | THYMUS |
---|---|---|
ALL | 27 | 96 |
subtype1 | 9 | 27 |
subtype2 | 5 | 22 |
subtype3 | 7 | 12 |
subtype4 | 4 | 27 |
subtype5 | 2 | 8 |
P value = 0.0494 (Fisher's exact test), Q value = 0.11
nPatients | FEMALE | MALE |
---|---|---|
ALL | 59 | 64 |
subtype1 | 15 | 21 |
subtype2 | 10 | 17 |
subtype3 | 15 | 4 |
subtype4 | 15 | 16 |
subtype5 | 4 | 6 |
P value = 0.0319 (Fisher's exact test), Q value = 0.085
nPatients | NO | YES |
---|---|---|
ALL | 81 | 42 |
subtype1 | 17 | 19 |
subtype2 | 21 | 6 |
subtype3 | 12 | 7 |
subtype4 | 25 | 6 |
subtype5 | 6 | 4 |
P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05
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 | 2 | 4 | 5 | 17 | 7 | 1 |
subtype2 | 9 | 14 | 0 | 2 | 2 | 0 |
subtype3 | 3 | 4 | 1 | 3 | 1 | 7 |
subtype4 | 1 | 13 | 8 | 6 | 2 | 1 |
subtype5 | 2 | 3 | 1 | 2 | 0 | 2 |
P value = 0.424 (Fisher's exact test), Q value = 0.58
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 13 | 6 | 102 |
subtype1 | 5 | 1 | 30 |
subtype2 | 1 | 1 | 25 |
subtype3 | 2 | 0 | 17 |
subtype4 | 5 | 3 | 21 |
subtype5 | 0 | 1 | 9 |
P value = 0.697 (Fisher's exact test), Q value = 0.83
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 9 | 100 |
subtype1 | 3 | 30 |
subtype2 | 1 | 21 |
subtype3 | 3 | 15 |
subtype4 | 2 | 27 |
subtype5 | 0 | 7 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 |
---|---|---|---|---|---|---|---|---|
Number of samples | 37 | 23 | 20 | 10 | 18 | 8 | 2 | 6 |
P value = 0.0285 (logrank test), Q value = 0.078
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 121 | 9 | 0.5 - 150.4 (41.2) |
subtype1 | 37 | 0 | 10.7 - 150.4 (51.7) |
subtype2 | 23 | 2 | 1.9 - 112.1 (42.3) |
subtype3 | 20 | 5 | 1.6 - 133.8 (49.6) |
subtype4 | 10 | 2 | 12.5 - 120.4 (27.7) |
subtype5 | 17 | 0 | 0.5 - 150.0 (34.6) |
subtype6 | 8 | 0 | 9.5 - 52.8 (33.7) |
subtype8 | 6 | 0 | 12.7 - 54.1 (49.7) |
P value = 0.00163 (Kruskal-Wallis (anova)), Q value = 0.0077
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 121 | 58.2 (13.1) |
subtype1 | 37 | 53.9 (12.6) |
subtype2 | 23 | 66.6 (9.6) |
subtype3 | 20 | 51.4 (14.2) |
subtype4 | 10 | 60.7 (12.5) |
subtype5 | 17 | 58.9 (11.6) |
subtype6 | 8 | 59.8 (14.4) |
subtype8 | 6 | 67.3 (5.9) |
P value = 0.604 (Fisher's exact test), Q value = 0.74
nPatients | ANTERIOR MEDIASTINUM | THYMUS |
---|---|---|
ALL | 26 | 96 |
subtype1 | 6 | 31 |
subtype2 | 4 | 19 |
subtype3 | 7 | 13 |
subtype4 | 2 | 8 |
subtype5 | 3 | 15 |
subtype6 | 3 | 5 |
subtype8 | 1 | 5 |
P value = 0.914 (Fisher's exact test), Q value = 0.97
nPatients | FEMALE | MALE |
---|---|---|
ALL | 59 | 63 |
subtype1 | 19 | 18 |
subtype2 | 9 | 14 |
subtype3 | 10 | 10 |
subtype4 | 5 | 5 |
subtype5 | 9 | 9 |
subtype6 | 3 | 5 |
subtype8 | 4 | 2 |
P value = 0.0477 (Fisher's exact test), Q value = 0.11
nPatients | NO | YES |
---|---|---|
ALL | 79 | 43 |
subtype1 | 24 | 13 |
subtype2 | 18 | 5 |
subtype3 | 9 | 11 |
subtype4 | 3 | 7 |
subtype5 | 14 | 4 |
subtype6 | 6 | 2 |
subtype8 | 5 | 1 |
P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 37 | 14 | 31 | 12 | 11 |
subtype1 | 0 | 7 | 13 | 15 | 2 | 0 |
subtype2 | 13 | 8 | 0 | 0 | 1 | 1 |
subtype3 | 1 | 2 | 1 | 10 | 6 | 0 |
subtype4 | 0 | 0 | 0 | 0 | 1 | 9 |
subtype5 | 1 | 15 | 0 | 2 | 0 | 0 |
subtype6 | 1 | 5 | 0 | 2 | 0 | 0 |
subtype8 | 1 | 0 | 0 | 2 | 2 | 1 |
P value = 0.534 (Fisher's exact test), Q value = 0.7
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 13 | 6 | 101 |
subtype1 | 2 | 5 | 30 |
subtype2 | 4 | 1 | 18 |
subtype3 | 2 | 0 | 18 |
subtype4 | 2 | 0 | 8 |
subtype5 | 2 | 0 | 16 |
subtype6 | 0 | 0 | 7 |
subtype8 | 1 | 0 | 4 |
P value = 0.0588 (Fisher's exact test), Q value = 0.13
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 9 | 99 |
subtype1 | 1 | 32 |
subtype2 | 0 | 21 |
subtype3 | 4 | 14 |
subtype4 | 2 | 8 |
subtype5 | 1 | 14 |
subtype6 | 1 | 5 |
subtype8 | 0 | 5 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 31 | 25 | 34 |
P value = 0.424 (logrank test), Q value = 0.58
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 89 | 8 | 1.6 - 150.4 (34.6) |
subtype1 | 30 | 4 | 1.6 - 150.0 (33.5) |
subtype2 | 25 | 2 | 4.1 - 97.4 (38.3) |
subtype3 | 34 | 2 | 9.5 - 150.4 (32.9) |
P value = 4.97e-05 (Kruskal-Wallis (anova)), Q value = 0.00033
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 = 0.583 (Fisher's exact test), Q value = 0.73
nPatients | ANTERIOR MEDIASTINUM | THYMUS |
---|---|---|
ALL | 22 | 68 |
subtype1 | 6 | 25 |
subtype2 | 8 | 17 |
subtype3 | 8 | 26 |
P value = 0.32 (Fisher's exact test), Q value = 0.48
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 = 0.58
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 = 7.3e-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 = 0.265 (Fisher's exact test), Q value = 0.44
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 = 0.58 (Fisher's exact test), Q value = 0.73
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 = 0.0888 (logrank test), Q value = 0.19
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 89 | 8 | 1.6 - 150.4 (34.6) |
subtype1 | 16 | 1 | 13.9 - 107.4 (30.3) |
subtype2 | 22 | 2 | 4.1 - 95.7 (35.3) |
subtype3 | 31 | 1 | 9.5 - 150.4 (50.8) |
subtype4 | 20 | 4 | 1.6 - 120.4 (27.7) |
P value = 0.00733 (Kruskal-Wallis (anova)), Q value = 0.029
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 = 0.935 (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 = 0.749 (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 = 0.0464 (Fisher's exact test), Q value = 0.11
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 = 7.3e-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 = 0.778 (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 = 0.265 (Fisher's exact test), Q value = 0.44
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 | 30 | 30 | 14 |
P value = 0.109 (logrank test), Q value = 0.21
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 119 | 9 | 0.5 - 150.4 (40.1) |
subtype1 | 46 | 5 | 1.6 - 150.4 (50.3) |
subtype2 | 30 | 0 | 9.5 - 150.0 (39.2) |
subtype3 | 29 | 2 | 0.5 - 120.4 (41.2) |
subtype4 | 14 | 2 | 12.5 - 58.8 (29.3) |
P value = 0.0186 (Kruskal-Wallis (anova)), Q value = 0.057
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 119 | 57.9 (13.1) |
subtype1 | 46 | 53.1 (14.3) |
subtype2 | 30 | 59.0 (10.0) |
subtype3 | 29 | 62.8 (12.9) |
subtype4 | 14 | 61.1 (10.6) |
P value = 0.937 (Fisher's exact test), Q value = 0.97
nPatients | ANTERIOR MEDIASTINUM | THYMUS |
---|---|---|
ALL | 27 | 93 |
subtype1 | 12 | 34 |
subtype2 | 6 | 24 |
subtype3 | 6 | 24 |
subtype4 | 3 | 11 |
P value = 0.309 (Fisher's exact test), Q value = 0.48
nPatients | FEMALE | MALE |
---|---|---|
ALL | 57 | 63 |
subtype1 | 20 | 26 |
subtype2 | 13 | 17 |
subtype3 | 14 | 16 |
subtype4 | 10 | 4 |
P value = 0.0158 (Fisher's exact test), Q value = 0.053
nPatients | NO | YES |
---|---|---|
ALL | 78 | 42 |
subtype1 | 24 | 22 |
subtype2 | 25 | 5 |
subtype3 | 22 | 8 |
subtype4 | 7 | 7 |
P value = 1e-05 (Fisher's exact test), Q value = 7.3e-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 | 6 | 0 | 0 |
subtype3 | 10 | 16 | 0 | 1 | 1 | 2 |
subtype4 | 1 | 0 | 0 | 1 | 3 | 9 |
P value = 0.911 (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 | 24 |
subtype3 | 4 | 1 | 25 |
subtype4 | 2 | 0 | 12 |
P value = 0.114 (Fisher's exact test), Q value = 0.22
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 10 | 96 |
subtype1 | 4 | 35 |
subtype2 | 3 | 24 |
subtype3 | 0 | 26 |
subtype4 | 3 | 11 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 48 | 42 | 20 | 10 |
P value = 0.269 (logrank test), Q value = 0.44
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 119 | 9 | 0.5 - 150.4 (40.1) |
subtype1 | 48 | 5 | 1.6 - 150.4 (50.2) |
subtype2 | 41 | 1 | 0.5 - 150.0 (36.6) |
subtype3 | 20 | 1 | 12.7 - 112.1 (47.0) |
subtype4 | 10 | 2 | 12.5 - 120.4 (27.7) |
P value = 0.0033 (Kruskal-Wallis (anova)), Q value = 0.014
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 = 0.99
nPatients | ANTERIOR MEDIASTINUM | THYMUS |
---|---|---|
ALL | 27 | 93 |
subtype1 | 12 | 36 |
subtype2 | 9 | 33 |
subtype3 | 4 | 16 |
subtype4 | 2 | 8 |
P value = 0.821 (Fisher's exact test), Q value = 0.91
nPatients | FEMALE | MALE |
---|---|---|
ALL | 57 | 63 |
subtype1 | 21 | 27 |
subtype2 | 20 | 22 |
subtype3 | 10 | 10 |
subtype4 | 6 | 4 |
P value = 0.00173 (Fisher's exact test), Q value = 0.0077
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 = 7.3e-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 = 0.411 (Fisher's exact test), Q value = 0.58
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 = 0.44
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 |
---|---|---|---|---|
Number of samples | 57 | 61 | 5 | 1 |
P value = 0.00857 (logrank test), Q value = 0.03
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 122 | 9 | 0.5 - 150.4 (41.7) |
subtype1 | 57 | 6 | 1.6 - 150.4 (48.7) |
subtype2 | 60 | 1 | 0.5 - 150.0 (39.2) |
subtype3 | 5 | 2 | 25.4 - 82.7 (52.9) |
P value = 0.0475 (Kruskal-Wallis (anova)), Q value = 0.11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 122 | 58.0 (13.0) |
subtype1 | 57 | 55.3 (14.4) |
subtype2 | 60 | 61.1 (11.2) |
subtype3 | 5 | 52.2 (8.1) |
P value = 0.561 (Fisher's exact test), Q value = 0.72
nPatients | ANTERIOR MEDIASTINUM | THYMUS |
---|---|---|
ALL | 27 | 96 |
subtype1 | 15 | 42 |
subtype2 | 11 | 50 |
subtype3 | 1 | 4 |
P value = 0.952 (Fisher's exact test), Q value = 0.98
nPatients | FEMALE | MALE |
---|---|---|
ALL | 60 | 63 |
subtype1 | 29 | 28 |
subtype2 | 29 | 32 |
subtype3 | 2 | 3 |
P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05
nPatients | NO | YES |
---|---|---|
ALL | 80 | 43 |
subtype1 | 29 | 28 |
subtype2 | 51 | 10 |
subtype3 | 0 | 5 |
P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 14 | 31 | 12 | 11 |
subtype1 | 3 | 5 | 10 | 22 | 7 | 10 |
subtype2 | 14 | 32 | 3 | 8 | 3 | 1 |
subtype3 | 0 | 1 | 1 | 1 | 2 | 0 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 13 | 6 | 102 |
subtype1 | 6 | 3 | 47 |
subtype2 | 7 | 3 | 50 |
subtype3 | 0 | 0 | 5 |
P value = 0.119 (Fisher's exact test), Q value = 0.22
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 10 | 99 |
subtype1 | 8 | 43 |
subtype2 | 2 | 52 |
subtype3 | 0 | 4 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 27 | 18 | 29 | 7 | 16 | 27 |
P value = 0.0208 (logrank test), Q value = 0.059
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 123 | 9 | 0.5 - 150.4 (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 - 150.4 (37.6) |
subtype4 | 7 | 2 | 12.5 - 58.8 (28.0) |
subtype5 | 16 | 0 | 12.7 - 112.1 (43.8) |
subtype6 | 27 | 0 | 9.5 - 138.9 (38.3) |
P value = 0.00796 (Kruskal-Wallis (anova)), Q value = 0.03
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 = 0.56
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 = 0.164 (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 = 0.00054 (Fisher's exact test), Q value = 0.0027
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 = 7.3e-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 = 0.822 (Fisher's exact test), Q value = 0.91
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 = 0.138 (Fisher's exact test), Q value = 0.25
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 | 4 |
---|---|---|---|---|
Number of samples | 28 | 51 | 44 | 1 |
P value = 0.0183 (logrank test), Q value = 0.057
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 122 | 9 | 0.5 - 150.4 (41.7) |
subtype1 | 28 | 0 | 10.7 - 138.9 (37.1) |
subtype2 | 50 | 1 | 0.5 - 150.0 (38.1) |
subtype3 | 44 | 8 | 1.6 - 150.4 (50.2) |
P value = 0.00872 (Kruskal-Wallis (anova)), Q value = 0.03
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 122 | 58.2 (13.1) |
subtype1 | 28 | 53.9 (12.6) |
subtype2 | 50 | 62.6 (11.4) |
subtype3 | 44 | 56.0 (13.9) |
P value = 0.786 (Fisher's exact test), Q value = 0.9
nPatients | ANTERIOR MEDIASTINUM | THYMUS |
---|---|---|
ALL | 27 | 96 |
subtype1 | 5 | 23 |
subtype2 | 11 | 40 |
subtype3 | 11 | 33 |
P value = 0.641 (Fisher's exact test), Q value = 0.78
nPatients | FEMALE | MALE |
---|---|---|
ALL | 59 | 64 |
subtype1 | 15 | 13 |
subtype2 | 22 | 29 |
subtype3 | 22 | 22 |
P value = 3e-04 (Fisher's exact test), Q value = 0.0017
nPatients | NO | YES |
---|---|---|
ALL | 81 | 42 |
subtype1 | 20 | 8 |
subtype2 | 42 | 9 |
subtype3 | 19 | 25 |
P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05
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 | 0 | 4 | 14 | 9 | 1 | 0 |
subtype2 | 14 | 29 | 0 | 5 | 2 | 1 |
subtype3 | 3 | 5 | 1 | 16 | 9 | 10 |
P value = 0.0747 (Fisher's exact test), Q value = 0.16
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 13 | 6 | 102 |
subtype1 | 1 | 4 | 23 |
subtype2 | 6 | 2 | 42 |
subtype3 | 6 | 0 | 37 |
P value = 0.0916 (Fisher's exact test), Q value = 0.19
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 10 | 99 |
subtype1 | 1 | 24 |
subtype2 | 2 | 42 |
subtype3 | 7 | 33 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 27 | 33 | 36 | 28 |
P value = 0.155 (logrank test), Q value = 0.27
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 123 | 9 | 0.5 - 150.4 (41.2) |
subtype1 | 27 | 3 | 12.7 - 123.7 (52.9) |
subtype2 | 32 | 1 | 0.5 - 112.1 (36.9) |
subtype3 | 36 | 5 | 1.6 - 150.4 (29.3) |
subtype4 | 28 | 0 | 9.5 - 150.0 (43.0) |
P value = 0.0197 (Kruskal-Wallis (anova)), Q value = 0.058
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 123 | 58.2 (13.0) |
subtype1 | 27 | 51.8 (14.4) |
subtype2 | 32 | 63.3 (10.4) |
subtype3 | 36 | 58.0 (13.4) |
subtype4 | 28 | 58.6 (11.7) |
P value = 0.296 (Fisher's exact test), Q value = 0.46
nPatients | ANTERIOR MEDIASTINUM | THYMUS |
---|---|---|
ALL | 27 | 97 |
subtype1 | 4 | 23 |
subtype2 | 6 | 27 |
subtype3 | 12 | 24 |
subtype4 | 5 | 23 |
P value = 0.0475 (Fisher's exact test), Q value = 0.11
nPatients | FEMALE | MALE |
---|---|---|
ALL | 60 | 64 |
subtype1 | 8 | 19 |
subtype2 | 14 | 19 |
subtype3 | 23 | 13 |
subtype4 | 15 | 13 |
P value = 0.00045 (Fisher's exact test), Q value = 0.0024
nPatients | NO | YES |
---|---|---|
ALL | 81 | 43 |
subtype1 | 13 | 14 |
subtype2 | 27 | 6 |
subtype3 | 17 | 19 |
subtype4 | 24 | 4 |
P value = 1e-05 (Fisher's exact test), Q value = 7.3e-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 | 3 | 2 |
subtype2 | 12 | 16 | 0 | 1 | 3 | 1 |
subtype3 | 3 | 2 | 9 | 8 | 6 | 8 |
subtype4 | 2 | 16 | 3 | 7 | 0 | 0 |
P value = 0.881 (Fisher's exact test), Q value = 0.97
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 13 | 6 | 103 |
subtype1 | 4 | 1 | 21 |
subtype2 | 4 | 1 | 28 |
subtype3 | 2 | 2 | 32 |
subtype4 | 3 | 2 | 22 |
P value = 0.0967 (Fisher's exact test), Q value = 0.19
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 10 | 100 |
subtype1 | 1 | 20 |
subtype2 | 1 | 28 |
subtype3 | 7 | 28 |
subtype4 | 1 | 24 |
-
Cluster data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THYM-TP/22541006/THYM-TP.mergedcluster.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/THYM-TP/22507339/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.