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 10 clinical features across 134 patients, 43 significant findings detected with P value < 0.05 and Q value < 0.25.
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4 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', and 'RADIATION_THERAPY'.
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4 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'RADIATION_THERAPY', and 'ETHNICITY'.
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CNMF clustering analysis on RPPA data identified 5 subtypes that correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'RADIATION_THERAPY'.
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Consensus hierarchical clustering analysis on RPPA data identified 3 subtypes that correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_M_STAGE', and 'RADIATION_THERAPY'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 6 subtypes that correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', and 'RADIATION_THERAPY'.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 7 subtypes that correlate to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', and 'RADIATION_THERAPY'.
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3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', and 'RADIATION_THERAPY'.
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3 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', and 'RADIATION_THERAPY'.
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3 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'RADIATION_THERAPY'.
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6 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'RADIATION_THERAPY'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
RADIATION THERAPY |
KARNOFSKY PERFORMANCE SCORE |
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 | Kruskal-Wallis (anova) | Fisher's exact test | Fisher's exact test |
Copy Number Ratio CNMF subtypes |
0.4 (0.634) |
0.0143 (0.0525) |
0.0205 (0.0602) |
0.116 (0.231) |
0.739 (0.913) |
0.579 (0.761) |
0.00022 (0.00183) |
0.866 (0.951) |
0.958 (0.986) |
0.97 (0.986) |
METHLYATION CNMF |
0.47 (0.653) |
0.0385 (0.0916) |
0.0059 (0.0257) |
0.049 (0.114) |
0.286 (0.51) |
0.828 (0.949) |
0.0001 (0.00122) |
0.477 (0.653) |
0.355 (0.582) |
0.0337 (0.0842) |
RPPA CNMF subtypes |
0.855 (0.951) |
0.025 (0.0694) |
8e-05 (0.00114) |
0.00116 (0.00737) |
0.0157 (0.0526) |
0.0818 (0.17) |
0.0022 (0.0129) |
0.753 (0.918) |
0.976 (0.986) |
0.8 (0.942) |
RPPA cHierClus subtypes |
0.427 (0.652) |
0.031 (0.0794) |
0.00118 (0.00737) |
0.301 (0.511) |
0.204 (0.393) |
0.00667 (0.0278) |
0.00018 (0.00173) |
0.634 (0.813) |
0.835 (0.949) |
1 (1.00) |
RNAseq CNMF subtypes |
0.438 (0.652) |
0.0193 (0.0584) |
0.0191 (0.0584) |
0.0042 (0.0211) |
0.801 (0.942) |
0.00453 (0.0216) |
2e-05 (0.000667) |
0.8 (0.942) |
0.935 (0.986) |
0.185 (0.363) |
RNAseq cHierClus subtypes |
0.0189 (0.0584) |
0.0551 (0.125) |
0.00261 (0.0145) |
0.00787 (0.0315) |
0.221 (0.41) |
0.0249 (0.0694) |
8e-05 (0.00114) |
0.47 (0.653) |
0.961 (0.986) |
0.417 (0.652) |
MIRSEQ CNMF |
0.944 (0.986) |
0.213 (0.402) |
0.061 (0.136) |
0.0302 (0.0794) |
0.297 (0.511) |
0.0257 (0.0696) |
0.00011 (0.00122) |
0.481 (0.653) |
0.976 (0.986) |
0.444 (0.652) |
MIRSEQ CHIERARCHICAL |
0.734 (0.913) |
0.00522 (0.0237) |
0.0004 (0.00308) |
0.00423 (0.0211) |
0.253 (0.46) |
0.0158 (0.0526) |
1e-05 (0.000667) |
0.603 (0.783) |
0.86 (0.951) |
0.393 (0.633) |
MIRseq Mature CNMF subtypes |
0.483 (0.653) |
0.0147 (0.0525) |
7e-05 (0.00114) |
0.00061 (0.00436) |
0.296 (0.511) |
0.0777 (0.165) |
2e-05 (0.000667) |
0.31 (0.516) |
0.821 (0.949) |
0.48 (0.653) |
MIRseq Mature cHierClus subtypes |
0.431 (0.652) |
0.0356 (0.0869) |
0.00019 (0.00173) |
0.0145 (0.0525) |
0.0659 (0.143) |
0.105 (0.214) |
3e-05 (0.00075) |
0.574 (0.761) |
0.963 (0.986) |
0.733 (0.913) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 43 | 33 | 45 | 13 |
P value = 0.4 (logrank test), Q value = 0.63
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 134 | 4 | 0.1 - 244.5 (41.5) |
subtype1 | 43 | 2 | 0.1 - 225.6 (31.9) |
subtype2 | 33 | 0 | 0.4 - 232.8 (36.8) |
subtype3 | 45 | 2 | 0.6 - 244.5 (73.3) |
subtype4 | 13 | 0 | 0.5 - 230.9 (75.2) |
P value = 0.0143 (Kruskal-Wallis (anova)), Q value = 0.053
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 32.0 (9.3) |
subtype1 | 43 | 33.0 (8.1) |
subtype2 | 33 | 34.5 (7.9) |
subtype3 | 45 | 29.9 (10.9) |
subtype4 | 13 | 29.5 (9.0) |
P value = 0.0205 (Fisher's exact test), Q value = 0.06
nPatients | IS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 11 | 4 | 6 | 1 | 1 | 2 | 1 | 6 | 5 |
subtype1 | 9 | 4 | 15 | 5 | 1 | 4 | 0 | 1 | 0 | 1 | 1 | 1 |
subtype2 | 11 | 7 | 6 | 3 | 0 | 1 | 1 | 0 | 0 | 0 | 1 | 0 |
subtype3 | 21 | 4 | 5 | 2 | 2 | 0 | 0 | 0 | 1 | 0 | 4 | 3 |
subtype4 | 5 | 3 | 0 | 1 | 1 | 1 | 0 | 0 | 1 | 0 | 0 | 1 |
P value = 0.116 (Fisher's exact test), Q value = 0.23
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 76 | 51 | 6 |
subtype1 | 27 | 13 | 2 |
subtype2 | 21 | 11 | 1 |
subtype3 | 25 | 17 | 3 |
subtype4 | 3 | 10 | 0 |
P value = 0.739 (Fisher's exact test), Q value = 0.91
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 46 | 13 |
subtype1 | 11 | 5 |
subtype2 | 10 | 3 |
subtype3 | 21 | 4 |
subtype4 | 4 | 1 |
P value = 0.579 (Fisher's exact test), Q value = 0.76
nPatients | 0 | 1 |
---|---|---|
ALL | 115 | 4 |
subtype1 | 36 | 1 |
subtype2 | 29 | 0 |
subtype3 | 38 | 3 |
subtype4 | 12 | 0 |
P value = 0.00022 (Fisher's exact test), Q value = 0.0018
nPatients | NO | YES |
---|---|---|
ALL | 111 | 21 |
subtype1 | 38 | 5 |
subtype2 | 19 | 13 |
subtype3 | 43 | 2 |
subtype4 | 11 | 1 |
P value = 0.866 (Kruskal-Wallis (anova)), Q value = 0.95
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 102 | 95.0 (5.9) |
subtype1 | 29 | 94.5 (5.7) |
subtype2 | 26 | 95.8 (5.0) |
subtype3 | 34 | 94.7 (6.6) |
subtype4 | 13 | 95.4 (6.6) |
P value = 0.958 (Fisher's exact test), Q value = 0.99
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 4 | 6 | 119 |
subtype1 | 2 | 3 | 36 |
subtype2 | 1 | 1 | 29 |
subtype3 | 1 | 2 | 41 |
subtype4 | 0 | 0 | 13 |
P value = 0.97 (Fisher's exact test), Q value = 0.99
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 111 |
subtype1 | 3 | 35 |
subtype2 | 3 | 28 |
subtype3 | 5 | 36 |
subtype4 | 1 | 12 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 43 | 20 | 32 | 39 |
P value = 0.47 (logrank test), Q value = 0.65
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 134 | 4 | 0.1 - 244.5 (41.5) |
subtype1 | 43 | 2 | 0.1 - 232.8 (31.9) |
subtype2 | 20 | 0 | 0.5 - 203.3 (47.2) |
subtype3 | 32 | 2 | 0.6 - 230.9 (80.8) |
subtype4 | 39 | 0 | 0.4 - 244.5 (44.5) |
P value = 0.0385 (Kruskal-Wallis (anova)), Q value = 0.092
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 32.0 (9.3) |
subtype1 | 43 | 33.9 (8.4) |
subtype2 | 20 | 31.9 (7.7) |
subtype3 | 32 | 28.8 (10.6) |
subtype4 | 39 | 32.5 (9.5) |
P value = 0.0059 (Fisher's exact test), Q value = 0.026
nPatients | IS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 11 | 4 | 6 | 1 | 1 | 2 | 1 | 6 | 5 |
subtype1 | 8 | 9 | 14 | 3 | 0 | 5 | 0 | 1 | 0 | 1 | 1 | 0 |
subtype2 | 7 | 4 | 5 | 2 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
subtype3 | 12 | 2 | 3 | 4 | 3 | 1 | 0 | 0 | 1 | 0 | 3 | 2 |
subtype4 | 19 | 3 | 4 | 2 | 1 | 0 | 0 | 0 | 1 | 0 | 2 | 3 |
P value = 0.049 (Fisher's exact test), Q value = 0.11
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 76 | 51 | 6 |
subtype1 | 26 | 14 | 2 |
subtype2 | 11 | 9 | 0 |
subtype3 | 12 | 19 | 1 |
subtype4 | 27 | 9 | 3 |
P value = 0.286 (Fisher's exact test), Q value = 0.51
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 46 | 13 |
subtype1 | 11 | 7 |
subtype2 | 6 | 1 |
subtype3 | 15 | 3 |
subtype4 | 14 | 2 |
P value = 0.828 (Fisher's exact test), Q value = 0.95
nPatients | 0 | 1 |
---|---|---|
ALL | 115 | 4 |
subtype1 | 38 | 1 |
subtype2 | 19 | 0 |
subtype3 | 28 | 1 |
subtype4 | 30 | 2 |
P value = 1e-04 (Fisher's exact test), Q value = 0.0012
nPatients | NO | YES |
---|---|---|
ALL | 111 | 21 |
subtype1 | 31 | 12 |
subtype2 | 12 | 7 |
subtype3 | 32 | 0 |
subtype4 | 36 | 2 |
P value = 0.477 (Kruskal-Wallis (anova)), Q value = 0.65
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 102 | 95.0 (5.9) |
subtype1 | 33 | 96.1 (5.6) |
subtype2 | 16 | 94.4 (5.1) |
subtype3 | 24 | 93.3 (7.6) |
subtype4 | 29 | 95.5 (5.1) |
P value = 0.355 (Fisher's exact test), Q value = 0.58
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 4 | 6 | 119 |
subtype1 | 2 | 0 | 40 |
subtype2 | 1 | 1 | 18 |
subtype3 | 0 | 3 | 29 |
subtype4 | 1 | 2 | 32 |
P value = 0.0337 (Fisher's exact test), Q value = 0.084
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 111 |
subtype1 | 1 | 41 |
subtype2 | 5 | 15 |
subtype3 | 2 | 27 |
subtype4 | 4 | 28 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 44 | 7 | 8 | 29 | 16 |
P value = 0.855 (logrank test), Q value = 0.95
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 104 | 4 | 0.1 - 244.5 (45.3) |
subtype1 | 44 | 1 | 0.1 - 232.8 (32.5) |
subtype2 | 7 | 0 | 15.5 - 203.3 (37.0) |
subtype3 | 8 | 0 | 22.2 - 172.0 (75.4) |
subtype4 | 29 | 2 | 0.6 - 244.5 (73.3) |
subtype5 | 16 | 1 | 6.9 - 230.9 (89.0) |
P value = 0.025 (Kruskal-Wallis (anova)), Q value = 0.069
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 104 | 32.0 (9.0) |
subtype1 | 44 | 34.3 (8.5) |
subtype2 | 7 | 29.9 (4.9) |
subtype3 | 8 | 34.1 (7.0) |
subtype4 | 29 | 31.2 (10.8) |
subtype5 | 16 | 26.9 (7.1) |
P value = 8e-05 (Fisher's exact test), Q value = 0.0011
nPatients | IS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 38 | 13 | 21 | 8 | 4 | 3 | 1 | 1 | 1 | 5 | 4 |
subtype1 | 14 | 11 | 12 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 2 |
subtype2 | 2 | 0 | 2 | 0 | 0 | 1 | 1 | 0 | 0 | 1 | 0 |
subtype3 | 2 | 0 | 0 | 4 | 0 | 1 | 0 | 0 | 1 | 0 | 0 |
subtype4 | 14 | 2 | 4 | 0 | 1 | 0 | 0 | 1 | 0 | 2 | 2 |
subtype5 | 6 | 0 | 3 | 0 | 3 | 1 | 0 | 0 | 0 | 2 | 0 |
P value = 0.00116 (Fisher's exact test), Q value = 0.0074
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 61 | 40 | 3 |
subtype1 | 29 | 15 | 0 |
subtype2 | 4 | 3 | 0 |
subtype3 | 1 | 7 | 0 |
subtype4 | 21 | 5 | 3 |
subtype5 | 6 | 10 | 0 |
P value = 0.0157 (Fisher's exact test), Q value = 0.053
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 40 | 9 |
subtype1 | 16 | 0 |
subtype2 | 1 | 2 |
subtype3 | 5 | 2 |
subtype4 | 12 | 2 |
subtype5 | 6 | 3 |
P value = 0.0818 (Fisher's exact test), Q value = 0.17
nPatients | 0 | 1 |
---|---|---|
ALL | 90 | 4 |
subtype1 | 40 | 0 |
subtype2 | 6 | 0 |
subtype3 | 7 | 1 |
subtype4 | 22 | 3 |
subtype5 | 15 | 0 |
P value = 0.0022 (Fisher's exact test), Q value = 0.013
nPatients | NO | YES |
---|---|---|
ALL | 86 | 16 |
subtype1 | 29 | 13 |
subtype2 | 5 | 2 |
subtype3 | 8 | 0 |
subtype4 | 28 | 1 |
subtype5 | 16 | 0 |
P value = 0.753 (Kruskal-Wallis (anova)), Q value = 0.92
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 94.6 (5.7) |
subtype1 | 32 | 95.3 (5.7) |
subtype2 | 5 | 96.0 (5.5) |
subtype3 | 8 | 93.8 (5.2) |
subtype4 | 22 | 94.5 (6.0) |
subtype5 | 13 | 93.1 (6.3) |
P value = 0.976 (Fisher's exact test), Q value = 0.99
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 4 | 4 | 92 |
subtype1 | 3 | 2 | 36 |
subtype2 | 0 | 0 | 7 |
subtype3 | 0 | 0 | 8 |
subtype4 | 1 | 1 | 26 |
subtype5 | 0 | 1 | 15 |
P value = 0.8 (Fisher's exact test), Q value = 0.94
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 10 | 85 |
subtype1 | 5 | 36 |
subtype2 | 0 | 6 |
subtype3 | 0 | 8 |
subtype4 | 4 | 21 |
subtype5 | 1 | 14 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 50 | 19 | 35 |
P value = 0.427 (logrank test), Q value = 0.65
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 104 | 4 | 0.1 - 244.5 (45.3) |
subtype1 | 50 | 1 | 0.1 - 232.8 (36.7) |
subtype2 | 19 | 0 | 4.9 - 181.3 (75.2) |
subtype3 | 35 | 3 | 0.6 - 244.5 (81.4) |
P value = 0.031 (Kruskal-Wallis (anova)), Q value = 0.079
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 104 | 32.0 (9.0) |
subtype1 | 50 | 33.9 (8.2) |
subtype2 | 19 | 32.3 (10.9) |
subtype3 | 35 | 29.1 (8.5) |
P value = 0.00118 (Fisher's exact test), Q value = 0.0074
nPatients | IS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 38 | 13 | 21 | 8 | 4 | 3 | 1 | 1 | 1 | 5 | 4 |
subtype1 | 16 | 11 | 14 | 4 | 0 | 0 | 1 | 0 | 0 | 1 | 2 |
subtype2 | 6 | 0 | 3 | 4 | 0 | 1 | 0 | 0 | 1 | 1 | 1 |
subtype3 | 16 | 2 | 4 | 0 | 4 | 2 | 0 | 1 | 0 | 3 | 1 |
P value = 0.301 (Fisher's exact test), Q value = 0.51
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 61 | 40 | 3 |
subtype1 | 33 | 17 | 0 |
subtype2 | 10 | 8 | 1 |
subtype3 | 18 | 15 | 2 |
P value = 0.204 (Fisher's exact test), Q value = 0.39
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 40 | 9 |
subtype1 | 17 | 1 |
subtype2 | 8 | 3 |
subtype3 | 15 | 5 |
P value = 0.00667 (Fisher's exact test), Q value = 0.028
nPatients | 0 | 1 |
---|---|---|
ALL | 90 | 4 |
subtype1 | 45 | 0 |
subtype2 | 13 | 3 |
subtype3 | 32 | 1 |
P value = 0.00018 (Fisher's exact test), Q value = 0.0017
nPatients | NO | YES |
---|---|---|
ALL | 86 | 16 |
subtype1 | 33 | 15 |
subtype2 | 19 | 0 |
subtype3 | 34 | 1 |
P value = 0.634 (Kruskal-Wallis (anova)), Q value = 0.81
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 94.6 (5.7) |
subtype1 | 36 | 95.3 (5.6) |
subtype2 | 16 | 93.8 (6.2) |
subtype3 | 28 | 94.3 (5.7) |
P value = 0.835 (Fisher's exact test), Q value = 0.95
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 4 | 4 | 92 |
subtype1 | 3 | 2 | 42 |
subtype2 | 0 | 0 | 18 |
subtype3 | 1 | 2 | 32 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 10 | 85 |
subtype1 | 5 | 41 |
subtype2 | 2 | 14 |
subtype3 | 3 | 30 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
---|---|---|---|---|---|---|---|
Number of samples | 33 | 30 | 30 | 17 | 8 | 15 | 1 |
P value = 0.438 (logrank test), Q value = 0.65
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 133 | 4 | 0.1 - 244.5 (41.5) |
subtype1 | 33 | 1 | 0.1 - 232.8 (31.9) |
subtype2 | 30 | 0 | 0.4 - 203.3 (36.7) |
subtype3 | 30 | 3 | 0.6 - 230.9 (74.1) |
subtype4 | 17 | 0 | 8.9 - 244.5 (73.3) |
subtype5 | 8 | 0 | 0.5 - 75.2 (23.6) |
subtype6 | 15 | 0 | 4.9 - 216.9 (85.8) |
P value = 0.0193 (Kruskal-Wallis (anova)), Q value = 0.058
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 133 | 32.0 (9.3) |
subtype1 | 33 | 35.6 (9.3) |
subtype2 | 30 | 32.7 (6.6) |
subtype3 | 30 | 28.7 (10.3) |
subtype4 | 17 | 29.6 (8.4) |
subtype5 | 8 | 29.6 (6.1) |
subtype6 | 15 | 33.1 (12.2) |
P value = 0.0191 (Fisher's exact test), Q value = 0.058
nPatients | IS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 46 | 18 | 25 | 11 | 4 | 6 | 1 | 1 | 2 | 1 | 6 | 5 |
subtype1 | 6 | 8 | 9 | 4 | 0 | 1 | 0 | 1 | 0 | 0 | 1 | 2 |
subtype2 | 11 | 6 | 8 | 2 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
subtype3 | 12 | 1 | 3 | 2 | 3 | 3 | 0 | 0 | 1 | 1 | 2 | 1 |
subtype4 | 9 | 1 | 2 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 2 | 0 |
subtype5 | 1 | 1 | 2 | 3 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
subtype6 | 7 | 1 | 1 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 2 |
P value = 0.0042 (Fisher's exact test), Q value = 0.021
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 75 | 51 | 6 |
subtype1 | 18 | 13 | 1 |
subtype2 | 23 | 6 | 1 |
subtype3 | 10 | 19 | 1 |
subtype4 | 12 | 4 | 1 |
subtype5 | 2 | 6 | 0 |
subtype6 | 10 | 3 | 2 |
P value = 0.801 (Fisher's exact test), Q value = 0.94
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 45 | 13 |
subtype1 | 8 | 2 |
subtype2 | 9 | 1 |
subtype3 | 11 | 6 |
subtype4 | 7 | 2 |
subtype5 | 4 | 1 |
subtype6 | 6 | 1 |
P value = 0.00453 (Fisher's exact test), Q value = 0.022
nPatients | 0 | 1 |
---|---|---|
ALL | 114 | 4 |
subtype1 | 28 | 0 |
subtype2 | 27 | 0 |
subtype3 | 27 | 1 |
subtype4 | 16 | 0 |
subtype5 | 8 | 0 |
subtype6 | 8 | 3 |
P value = 2e-05 (Fisher's exact test), Q value = 0.00067
nPatients | NO | YES |
---|---|---|
ALL | 110 | 21 |
subtype1 | 25 | 8 |
subtype2 | 16 | 13 |
subtype3 | 30 | 0 |
subtype4 | 17 | 0 |
subtype5 | 7 | 0 |
subtype6 | 15 | 0 |
P value = 0.8 (Kruskal-Wallis (anova)), Q value = 0.94
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 102 | 95.0 (5.9) |
subtype1 | 26 | 95.8 (5.8) |
subtype2 | 23 | 95.7 (5.1) |
subtype3 | 22 | 93.2 (7.2) |
subtype4 | 14 | 95.7 (5.1) |
subtype5 | 7 | 95.7 (5.3) |
subtype6 | 10 | 94.0 (7.0) |
P value = 0.935 (Fisher's exact test), Q value = 0.99
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 4 | 5 | 119 |
subtype1 | 2 | 1 | 28 |
subtype2 | 1 | 1 | 27 |
subtype3 | 0 | 2 | 28 |
subtype4 | 1 | 0 | 15 |
subtype5 | 0 | 0 | 8 |
subtype6 | 0 | 1 | 13 |
P value = 0.185 (Fisher's exact test), Q value = 0.36
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 110 |
subtype1 | 1 | 29 |
subtype2 | 4 | 25 |
subtype3 | 2 | 26 |
subtype4 | 4 | 12 |
subtype5 | 1 | 7 |
subtype6 | 0 | 11 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
---|---|---|---|---|---|---|---|
Number of samples | 42 | 27 | 10 | 17 | 8 | 20 | 10 |
P value = 0.0189 (logrank test), Q value = 0.058
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 134 | 4 | 0.1 - 244.5 (41.5) |
subtype1 | 42 | 1 | 0.1 - 232.8 (30.7) |
subtype2 | 27 | 0 | 0.4 - 203.3 (36.6) |
subtype3 | 10 | 2 | 0.6 - 216.9 (56.6) |
subtype4 | 17 | 0 | 8.9 - 244.5 (75.6) |
subtype5 | 8 | 0 | 6.9 - 225.6 (50.0) |
subtype6 | 20 | 1 | 17.2 - 230.9 (81.4) |
subtype7 | 10 | 0 | 4.9 - 204.2 (48.3) |
P value = 0.0551 (Kruskal-Wallis (anova)), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 32.0 (9.3) |
subtype1 | 42 | 34.7 (8.7) |
subtype2 | 27 | 32.6 (6.9) |
subtype3 | 10 | 30.0 (8.4) |
subtype4 | 17 | 29.0 (8.3) |
subtype5 | 8 | 28.5 (6.8) |
subtype6 | 20 | 29.0 (11.9) |
subtype7 | 10 | 35.0 (13.2) |
P value = 0.00261 (Fisher's exact test), Q value = 0.014
nPatients | IS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 11 | 4 | 6 | 1 | 1 | 2 | 1 | 6 | 5 |
subtype1 | 9 | 9 | 12 | 5 | 0 | 1 | 0 | 1 | 0 | 0 | 1 | 2 |
subtype2 | 9 | 6 | 8 | 2 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
subtype3 | 5 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 1 |
subtype4 | 9 | 1 | 2 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 1 | 1 |
subtype5 | 1 | 0 | 0 | 2 | 1 | 3 | 0 | 0 | 0 | 1 | 0 | 0 |
subtype6 | 8 | 1 | 3 | 1 | 2 | 1 | 0 | 0 | 1 | 0 | 2 | 0 |
subtype7 | 5 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 1 |
P value = 0.00787 (Fisher's exact test), Q value = 0.031
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 76 | 51 | 6 |
subtype1 | 21 | 18 | 2 |
subtype2 | 22 | 5 | 0 |
subtype3 | 6 | 3 | 1 |
subtype4 | 11 | 4 | 2 |
subtype5 | 3 | 5 | 0 |
subtype6 | 6 | 14 | 0 |
subtype7 | 7 | 2 | 1 |
P value = 0.221 (Fisher's exact test), Q value = 0.41
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 46 | 13 |
subtype1 | 11 | 2 |
subtype2 | 9 | 1 |
subtype3 | 5 | 1 |
subtype4 | 8 | 2 |
subtype5 | 2 | 4 |
subtype6 | 9 | 3 |
subtype7 | 2 | 0 |
P value = 0.0249 (Fisher's exact test), Q value = 0.069
nPatients | 0 | 1 |
---|---|---|
ALL | 115 | 4 |
subtype1 | 37 | 0 |
subtype2 | 24 | 0 |
subtype3 | 8 | 1 |
subtype4 | 15 | 1 |
subtype5 | 7 | 1 |
subtype6 | 19 | 0 |
subtype7 | 5 | 1 |
P value = 8e-05 (Fisher's exact test), Q value = 0.0011
nPatients | NO | YES |
---|---|---|
ALL | 111 | 21 |
subtype1 | 32 | 9 |
subtype2 | 14 | 12 |
subtype3 | 10 | 0 |
subtype4 | 17 | 0 |
subtype5 | 8 | 0 |
subtype6 | 20 | 0 |
subtype7 | 10 | 0 |
P value = 0.47 (Kruskal-Wallis (anova)), Q value = 0.65
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 102 | 95.0 (5.9) |
subtype1 | 33 | 96.1 (5.6) |
subtype2 | 20 | 95.0 (5.1) |
subtype3 | 6 | 95.0 (8.4) |
subtype4 | 14 | 96.4 (5.0) |
subtype5 | 8 | 93.8 (5.2) |
subtype6 | 15 | 93.3 (8.2) |
subtype7 | 6 | 91.7 (4.1) |
P value = 0.961 (Fisher's exact test), Q value = 0.99
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 4 | 6 | 119 |
subtype1 | 2 | 2 | 36 |
subtype2 | 1 | 1 | 24 |
subtype3 | 0 | 1 | 9 |
subtype4 | 1 | 0 | 15 |
subtype5 | 0 | 0 | 8 |
subtype6 | 0 | 1 | 19 |
subtype7 | 0 | 1 | 8 |
P value = 0.417 (Fisher's exact test), Q value = 0.65
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 111 |
subtype1 | 2 | 37 |
subtype2 | 4 | 22 |
subtype3 | 0 | 9 |
subtype4 | 3 | 13 |
subtype5 | 1 | 7 |
subtype6 | 1 | 18 |
subtype7 | 1 | 5 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 50 | 55 | 29 |
P value = 0.944 (logrank test), Q value = 0.99
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 134 | 4 | 0.1 - 244.5 (41.5) |
subtype1 | 50 | 1 | 0.1 - 232.8 (35.2) |
subtype2 | 55 | 2 | 0.4 - 230.9 (45.2) |
subtype3 | 29 | 1 | 4.9 - 244.5 (71.2) |
P value = 0.213 (Kruskal-Wallis (anova)), Q value = 0.4
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 32.0 (9.3) |
subtype1 | 50 | 33.6 (8.4) |
subtype2 | 55 | 30.8 (9.4) |
subtype3 | 29 | 31.5 (10.4) |
P value = 0.061 (Fisher's exact test), Q value = 0.14
nPatients | IS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 11 | 4 | 6 | 1 | 1 | 2 | 1 | 6 | 5 |
subtype1 | 13 | 11 | 14 | 5 | 0 | 1 | 0 | 1 | 0 | 0 | 1 | 2 |
subtype2 | 18 | 6 | 9 | 6 | 3 | 4 | 1 | 0 | 1 | 1 | 3 | 1 |
subtype3 | 15 | 1 | 3 | 0 | 1 | 1 | 0 | 0 | 1 | 0 | 2 | 2 |
P value = 0.0302 (Fisher's exact test), Q value = 0.079
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 76 | 51 | 6 |
subtype1 | 31 | 17 | 1 |
subtype2 | 25 | 28 | 2 |
subtype3 | 20 | 6 | 3 |
P value = 0.297 (Fisher's exact test), Q value = 0.51
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 46 | 13 |
subtype1 | 16 | 2 |
subtype2 | 20 | 9 |
subtype3 | 10 | 2 |
P value = 0.0257 (Fisher's exact test), Q value = 0.07
nPatients | 0 | 1 |
---|---|---|
ALL | 115 | 4 |
subtype1 | 43 | 0 |
subtype2 | 51 | 1 |
subtype3 | 21 | 3 |
P value = 0.00011 (Fisher's exact test), Q value = 0.0012
nPatients | NO | YES |
---|---|---|
ALL | 111 | 21 |
subtype1 | 33 | 16 |
subtype2 | 49 | 5 |
subtype3 | 29 | 0 |
P value = 0.481 (Kruskal-Wallis (anova)), Q value = 0.65
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 102 | 95.0 (5.9) |
subtype1 | 37 | 95.9 (5.5) |
subtype2 | 44 | 94.5 (6.3) |
subtype3 | 21 | 94.3 (6.0) |
P value = 0.976 (Fisher's exact test), Q value = 0.99
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 4 | 6 | 119 |
subtype1 | 2 | 2 | 43 |
subtype2 | 1 | 3 | 51 |
subtype3 | 1 | 1 | 25 |
P value = 0.444 (Fisher's exact test), Q value = 0.65
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 111 |
subtype1 | 4 | 42 |
subtype2 | 4 | 49 |
subtype3 | 4 | 20 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 69 | 36 | 29 |
P value = 0.734 (logrank test), Q value = 0.91
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 134 | 4 | 0.1 - 244.5 (41.5) |
subtype1 | 69 | 1 | 0.1 - 232.8 (31.9) |
subtype2 | 36 | 2 | 0.6 - 230.9 (77.7) |
subtype3 | 29 | 1 | 4.9 - 244.5 (71.2) |
P value = 0.00522 (Kruskal-Wallis (anova)), Q value = 0.024
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 32.0 (9.3) |
subtype1 | 69 | 33.8 (8.1) |
subtype2 | 36 | 28.8 (9.9) |
subtype3 | 29 | 31.5 (10.4) |
P value = 4e-04 (Fisher's exact test), Q value = 0.0031
nPatients | IS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 11 | 4 | 6 | 1 | 1 | 2 | 1 | 6 | 5 |
subtype1 | 18 | 15 | 20 | 7 | 0 | 1 | 1 | 1 | 0 | 0 | 1 | 2 |
subtype2 | 13 | 2 | 3 | 4 | 3 | 4 | 0 | 0 | 1 | 1 | 3 | 1 |
subtype3 | 15 | 1 | 3 | 0 | 1 | 1 | 0 | 0 | 1 | 0 | 2 | 2 |
P value = 0.00423 (Fisher's exact test), Q value = 0.021
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 76 | 51 | 6 |
subtype1 | 43 | 23 | 2 |
subtype2 | 13 | 22 | 1 |
subtype3 | 20 | 6 | 3 |
P value = 0.253 (Fisher's exact test), Q value = 0.46
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 46 | 13 |
subtype1 | 20 | 3 |
subtype2 | 16 | 8 |
subtype3 | 10 | 2 |
P value = 0.0158 (Fisher's exact test), Q value = 0.053
nPatients | 0 | 1 |
---|---|---|
ALL | 115 | 4 |
subtype1 | 61 | 0 |
subtype2 | 33 | 1 |
subtype3 | 21 | 3 |
P value = 1e-05 (Fisher's exact test), Q value = 0.00067
nPatients | NO | YES |
---|---|---|
ALL | 111 | 21 |
subtype1 | 46 | 21 |
subtype2 | 36 | 0 |
subtype3 | 29 | 0 |
P value = 0.603 (Kruskal-Wallis (anova)), Q value = 0.78
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 102 | 95.0 (5.9) |
subtype1 | 53 | 95.7 (5.4) |
subtype2 | 28 | 94.3 (6.9) |
subtype3 | 21 | 94.3 (6.0) |
P value = 0.86 (Fisher's exact test), Q value = 0.95
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 4 | 6 | 119 |
subtype1 | 3 | 3 | 60 |
subtype2 | 0 | 2 | 34 |
subtype3 | 1 | 1 | 25 |
P value = 0.393 (Fisher's exact test), Q value = 0.63
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 111 |
subtype1 | 6 | 59 |
subtype2 | 2 | 32 |
subtype3 | 4 | 20 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 68 | 34 | 32 |
P value = 0.483 (logrank test), Q value = 0.65
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 134 | 4 | 0.1 - 244.5 (41.5) |
subtype1 | 68 | 1 | 0.1 - 232.8 (33.4) |
subtype2 | 34 | 1 | 6.9 - 230.9 (77.7) |
subtype3 | 32 | 2 | 0.6 - 244.5 (61.8) |
P value = 0.0147 (Kruskal-Wallis (anova)), Q value = 0.053
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 32.0 (9.3) |
subtype1 | 68 | 33.6 (8.0) |
subtype2 | 34 | 29.6 (10.7) |
subtype3 | 32 | 31.0 (9.9) |
P value = 7e-05 (Fisher's exact test), Q value = 0.0011
nPatients | IS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 11 | 4 | 6 | 1 | 1 | 2 | 1 | 6 | 5 |
subtype1 | 18 | 15 | 19 | 7 | 0 | 1 | 1 | 1 | 0 | 0 | 1 | 2 |
subtype2 | 11 | 2 | 4 | 4 | 3 | 4 | 0 | 0 | 1 | 1 | 3 | 0 |
subtype3 | 17 | 1 | 3 | 0 | 1 | 1 | 0 | 0 | 1 | 0 | 2 | 3 |
P value = 0.00061 (Fisher's exact test), Q value = 0.0044
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 76 | 51 | 6 |
subtype1 | 42 | 23 | 2 |
subtype2 | 12 | 22 | 0 |
subtype3 | 22 | 6 | 4 |
P value = 0.296 (Fisher's exact test), Q value = 0.51
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 46 | 13 |
subtype1 | 20 | 3 |
subtype2 | 14 | 7 |
subtype3 | 12 | 3 |
P value = 0.0777 (Fisher's exact test), Q value = 0.17
nPatients | 0 | 1 |
---|---|---|
ALL | 115 | 4 |
subtype1 | 60 | 0 |
subtype2 | 31 | 2 |
subtype3 | 24 | 2 |
P value = 2e-05 (Fisher's exact test), Q value = 0.00067
nPatients | NO | YES |
---|---|---|
ALL | 111 | 21 |
subtype1 | 46 | 20 |
subtype2 | 33 | 1 |
subtype3 | 32 | 0 |
P value = 0.31 (Kruskal-Wallis (anova)), Q value = 0.52
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 102 | 95.0 (5.9) |
subtype1 | 52 | 95.8 (5.4) |
subtype2 | 28 | 93.2 (7.2) |
subtype3 | 22 | 95.5 (5.1) |
P value = 0.821 (Fisher's exact test), Q value = 0.95
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 4 | 6 | 119 |
subtype1 | 3 | 3 | 59 |
subtype2 | 0 | 1 | 33 |
subtype3 | 1 | 2 | 27 |
P value = 0.48 (Fisher's exact test), Q value = 0.65
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 111 |
subtype1 | 6 | 58 |
subtype2 | 2 | 31 |
subtype3 | 4 | 22 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 33 | 36 | 17 | 19 | 19 | 10 |
P value = 0.431 (logrank test), Q value = 0.65
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 134 | 4 | 0.1 - 244.5 (41.5) |
subtype1 | 33 | 1 | 0.1 - 232.8 (29.4) |
subtype2 | 36 | 0 | 0.4 - 203.3 (36.7) |
subtype3 | 17 | 1 | 0.6 - 216.9 (81.4) |
subtype4 | 19 | 0 | 8.9 - 244.5 (71.2) |
subtype5 | 19 | 1 | 6.9 - 230.9 (80.2) |
subtype6 | 10 | 1 | 4.9 - 199.2 (51.3) |
P value = 0.0356 (Kruskal-Wallis (anova)), Q value = 0.087
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 32.0 (9.3) |
subtype1 | 33 | 33.7 (8.2) |
subtype2 | 36 | 34.0 (8.0) |
subtype3 | 17 | 30.1 (12.5) |
subtype4 | 19 | 33.2 (11.7) |
subtype5 | 19 | 28.2 (7.8) |
subtype6 | 10 | 27.2 (4.9) |
P value = 0.00019 (Fisher's exact test), Q value = 0.0017
nPatients | IS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 11 | 4 | 6 | 1 | 1 | 2 | 1 | 6 | 5 |
subtype1 | 8 | 8 | 12 | 3 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 |
subtype2 | 10 | 7 | 8 | 4 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 2 |
subtype3 | 8 | 2 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 1 |
subtype4 | 10 | 1 | 3 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 0 |
subtype5 | 4 | 0 | 2 | 3 | 3 | 4 | 0 | 0 | 1 | 1 | 1 | 0 |
subtype6 | 6 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 2 |
P value = 0.0145 (Fisher's exact test), Q value = 0.053
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 76 | 51 | 6 |
subtype1 | 18 | 13 | 1 |
subtype2 | 25 | 10 | 1 |
subtype3 | 8 | 8 | 1 |
subtype4 | 12 | 5 | 2 |
subtype5 | 5 | 14 | 0 |
subtype6 | 8 | 1 | 1 |
P value = 0.0659 (Fisher's exact test), Q value = 0.14
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 46 | 13 |
subtype1 | 12 | 1 |
subtype2 | 8 | 2 |
subtype3 | 9 | 2 |
subtype4 | 8 | 0 |
subtype5 | 6 | 6 |
subtype6 | 3 | 2 |
P value = 0.105 (Fisher's exact test), Q value = 0.21
nPatients | 0 | 1 |
---|---|---|
ALL | 115 | 4 |
subtype1 | 30 | 0 |
subtype2 | 31 | 0 |
subtype3 | 15 | 1 |
subtype4 | 16 | 1 |
subtype5 | 17 | 1 |
subtype6 | 6 | 1 |
P value = 3e-05 (Fisher's exact test), Q value = 0.00075
nPatients | NO | YES |
---|---|---|
ALL | 111 | 21 |
subtype1 | 24 | 8 |
subtype2 | 22 | 13 |
subtype3 | 17 | 0 |
subtype4 | 19 | 0 |
subtype5 | 19 | 0 |
subtype6 | 10 | 0 |
P value = 0.574 (Kruskal-Wallis (anova)), Q value = 0.76
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 102 | 95.0 (5.9) |
subtype1 | 25 | 95.6 (5.8) |
subtype2 | 28 | 95.7 (5.0) |
subtype3 | 12 | 94.2 (9.0) |
subtype4 | 15 | 94.0 (5.1) |
subtype5 | 17 | 93.5 (6.1) |
subtype6 | 5 | 98.0 (4.5) |
P value = 0.963 (Fisher's exact test), Q value = 0.99
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 4 | 6 | 119 |
subtype1 | 1 | 1 | 30 |
subtype2 | 2 | 2 | 30 |
subtype3 | 0 | 1 | 16 |
subtype4 | 1 | 0 | 16 |
subtype5 | 0 | 1 | 18 |
subtype6 | 0 | 1 | 9 |
P value = 0.733 (Fisher's exact test), Q value = 0.91
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 111 |
subtype1 | 2 | 30 |
subtype2 | 4 | 29 |
subtype3 | 1 | 15 |
subtype4 | 3 | 14 |
subtype5 | 1 | 17 |
subtype6 | 1 | 6 |
-
Cluster data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/TGCT-TP/22541961/TGCT-TP.mergedcluster.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/TGCT-TP/22507091/TGCT-TP.merged_data.txt
-
Number of patients = 134
-
Number of clustering approaches = 10
-
Number of selected clinical features = 10
-
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.