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 15 clinical features across 185 patients, 70 significant findings detected with P value < 0.05 and Q value < 0.25.
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3 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes correlate to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
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3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'RADIATION_THERAPY', 'HISTOLOGICAL_TYPE', 'NUMBER_PACK_YEARS_SMOKED', and 'RACE'.
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CNMF clustering analysis on RPPA data identified 5 subtypes that correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
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Consensus hierarchical clustering analysis on RPPA data identified 5 subtypes that correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', 'NUMBER_OF_LYMPH_NODES', and 'RACE'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
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3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'RADIATION_THERAPY', 'HISTOLOGICAL_TYPE', 'NUMBER_PACK_YEARS_SMOKED', and 'RACE'.
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4 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes correlate to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RADIATION_THERAPY', 'HISTOLOGICAL_TYPE', and 'RACE'.
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4 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'RADIATION_THERAPY', 'HISTOLOGICAL_TYPE', 'NUMBER_PACK_YEARS_SMOKED', and 'RACE'.
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3 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes correlate to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RADIATION_THERAPY', 'HISTOLOGICAL_TYPE', 'NUMBER_PACK_YEARS_SMOKED', and 'RACE'.
Clinical Features |
Statistical Tests |
Copy Number Ratio CNMF subtypes |
METHLYATION CNMF |
RPPA CNMF subtypes |
RPPA cHierClus subtypes |
RNAseq CNMF subtypes |
RNAseq cHierClus subtypes |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRseq Mature CNMF subtypes |
MIRseq Mature cHierClus subtypes |
Time to Death | logrank test |
0.127 (0.212) |
0.385 (0.489) |
0.186 (0.274) |
0.421 (0.51) |
0.859 (0.871) |
0.837 (0.866) |
0.603 (0.685) |
0.0174 (0.0441) |
0.313 (0.412) |
0.0496 (0.106) |
YEARS TO BIRTH | Kruskal-Wallis (anova) |
5.44e-05 (0.000233) |
3.09e-05 (0.00014) |
0.0149 (0.0385) |
0.000524 (0.00187) |
5.44e-06 (5.36e-05) |
6.96e-06 (5.36e-05) |
1.95e-06 (5.36e-05) |
1.85e-06 (5.36e-05) |
1.86e-05 (9.37e-05) |
3.12e-07 (4.69e-05) |
PATHOLOGIC STAGE | Fisher's exact test |
0.0567 (0.113) |
8e-05 (0.000333) |
0.0309 (0.0703) |
0.00946 (0.0253) |
5e-05 (0.000221) |
1e-05 (5.36e-05) |
2e-05 (9.37e-05) |
1e-05 (5.36e-05) |
0.00012 (0.000486) |
1e-05 (5.36e-05) |
PATHOLOGY T STAGE | Fisher's exact test |
0.00489 (0.0138) |
2e-05 (9.37e-05) |
0.00278 (0.00851) |
0.00317 (0.00951) |
1e-05 (5.36e-05) |
0.00193 (0.00642) |
2e-05 (9.37e-05) |
0.00083 (0.0029) |
0.00171 (0.00583) |
0.00018 (0.000692) |
PATHOLOGY N STAGE | Fisher's exact test |
0.219 (0.295) |
0.137 (0.218) |
0.283 (0.379) |
0.06 (0.117) |
0.00232 (0.00725) |
0.00496 (0.0138) |
0.0561 (0.113) |
0.0438 (0.0953) |
0.0958 (0.169) |
0.0065 (0.0177) |
PATHOLOGY M STAGE | Fisher's exact test |
0.554 (0.644) |
0.815 (0.849) |
0.0812 (0.15) |
0.0521 (0.107) |
0.775 (0.818) |
0.342 (0.439) |
0.632 (0.702) |
0.203 (0.287) |
0.213 (0.293) |
0.463 (0.551) |
GENDER | Fisher's exact test |
0.0829 (0.152) |
0.601 (0.685) |
0.647 (0.709) |
0.132 (0.217) |
0.64 (0.706) |
0.912 (0.912) |
0.748 (0.802) |
0.484 (0.571) |
0.911 (0.912) |
0.683 (0.737) |
RADIATION THERAPY | Fisher's exact test |
0.148 (0.229) |
0.0103 (0.0271) |
0.628 (0.702) |
0.142 (0.222) |
0.00015 (0.000592) |
0.00027 (0.00101) |
0.00197 (0.00642) |
0.00215 (0.00686) |
0.00359 (0.0104) |
0.00356 (0.0104) |
KARNOFSKY PERFORMANCE SCORE | Kruskal-Wallis (anova) |
0.329 (0.425) |
0.126 (0.212) |
0.39 (0.491) |
0.0874 (0.156) |
0.029 (0.068) |
0.0361 (0.0808) |
0.136 (0.218) |
0.116 (0.2) |
0.0578 (0.114) |
0.0516 (0.107) |
HISTOLOGICAL TYPE | Fisher's exact test |
1e-05 (5.36e-05) |
1e-05 (5.36e-05) |
1e-05 (5.36e-05) |
1e-05 (5.36e-05) |
1e-05 (5.36e-05) |
1e-05 (5.36e-05) |
1e-05 (5.36e-05) |
1e-05 (5.36e-05) |
1e-05 (5.36e-05) |
1e-05 (5.36e-05) |
NUMBER PACK YEARS SMOKED | Kruskal-Wallis (anova) |
0.194 (0.283) |
0.0432 (0.0953) |
0.395 (0.491) |
0.318 (0.414) |
0.0772 (0.147) |
0.125 (0.212) |
0.0198 (0.0496) |
0.136 (0.218) |
0.0226 (0.0538) |
0.021 (0.0509) |
RESIDUAL TUMOR | Fisher's exact test |
0.631 (0.702) |
0.78 (0.818) |
0.0712 (0.137) |
0.152 (0.233) |
0.85 (0.867) |
0.142 (0.222) |
0.562 (0.648) |
0.676 (0.735) |
0.312 (0.412) |
0.406 (0.5) |
NUMBER OF LYMPH NODES | Kruskal-Wallis (anova) |
0.205 (0.288) |
0.531 (0.622) |
0.412 (0.503) |
0.0309 (0.0703) |
0.166 (0.251) |
0.0507 (0.107) |
0.11 (0.193) |
0.21 (0.291) |
0.086 (0.155) |
0.0788 (0.148) |
RACE | Fisher's exact test |
1e-05 (5.36e-05) |
1e-05 (5.36e-05) |
0.00038 (0.00139) |
1e-05 (5.36e-05) |
1e-05 (5.36e-05) |
1e-05 (5.36e-05) |
1e-05 (5.36e-05) |
1e-05 (5.36e-05) |
1e-05 (5.36e-05) |
1e-05 (5.36e-05) |
ETHNICITY | Fisher's exact test |
0.844 (0.867) |
0.216 (0.295) |
0.198 (0.286) |
0.774 (0.818) |
0.0202 (0.0496) |
0.172 (0.258) |
0.396 (0.491) |
0.176 (0.262) |
0.447 (0.537) |
0.2 (0.286) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 65 | 44 | 75 |
P value = 0.127 (logrank test), Q value = 0.21
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 183 | 76 | 0.1 - 122.1 (13.2) |
subtype1 | 65 | 36 | 0.4 - 122.1 (13.4) |
subtype2 | 44 | 13 | 1.6 - 83.2 (15.5) |
subtype3 | 74 | 27 | 0.1 - 52.6 (12.7) |
P value = 5.44e-05 (Kruskal-Wallis (anova)), Q value = 0.00023
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 184 | 62.4 (11.9) |
subtype1 | 65 | 64.0 (12.4) |
subtype2 | 44 | 67.5 (11.5) |
subtype3 | 75 | 58.1 (10.2) |
P value = 0.0567 (Fisher's exact test), Q value = 0.11
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 8 | 5 | 6 | 1 | 47 | 31 | 25 | 14 | 9 | 7 | 5 | 4 |
subtype1 | 4 | 2 | 2 | 0 | 6 | 11 | 12 | 4 | 3 | 2 | 2 | 2 |
subtype2 | 4 | 2 | 1 | 0 | 12 | 9 | 3 | 2 | 2 | 3 | 0 | 1 |
subtype3 | 0 | 1 | 3 | 1 | 29 | 11 | 10 | 8 | 4 | 2 | 3 | 1 |
P value = 0.00489 (Fisher's exact test), Q value = 0.014
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 32 | 43 | 87 | 5 |
subtype1 | 16 | 8 | 30 | 0 |
subtype2 | 10 | 9 | 20 | 1 |
subtype3 | 6 | 26 | 37 | 4 |
P value = 0.219 (Fisher's exact test), Q value = 0.3
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 77 | 68 | 12 | 8 |
subtype1 | 18 | 29 | 5 | 2 |
subtype2 | 22 | 12 | 2 | 3 |
subtype3 | 37 | 27 | 5 | 3 |
P value = 0.554 (Fisher's exact test), Q value = 0.64
nPatients | 0 | 1 |
---|---|---|
ALL | 135 | 9 |
subtype1 | 37 | 4 |
subtype2 | 33 | 1 |
subtype3 | 65 | 4 |
P value = 0.0829 (Fisher's exact test), Q value = 0.15
nPatients | FEMALE | MALE |
---|---|---|
ALL | 27 | 157 |
subtype1 | 6 | 59 |
subtype2 | 11 | 33 |
subtype3 | 10 | 65 |
P value = 0.148 (Fisher's exact test), Q value = 0.23
nPatients | NO | YES |
---|---|---|
ALL | 124 | 42 |
subtype1 | 47 | 10 |
subtype2 | 30 | 9 |
subtype3 | 47 | 23 |
P value = 0.329 (Kruskal-Wallis (anova)), Q value = 0.43
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 68 | 73.8 (16.2) |
subtype1 | 9 | 75.6 (15.1) |
subtype2 | 10 | 79.0 (17.3) |
subtype3 | 49 | 72.4 (16.3) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | ESOPHAGUS ADENOCARCINOMA NOS | ESOPHAGUS SQUAMOUS CELL CARCINOMA |
---|---|---|
ALL | 88 | 96 |
subtype1 | 60 | 5 |
subtype2 | 27 | 17 |
subtype3 | 1 | 74 |
P value = 0.194 (Kruskal-Wallis (anova)), Q value = 0.28
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 98 | 34.5 (21.5) |
subtype1 | 33 | 36.2 (22.9) |
subtype2 | 22 | 40.0 (24.1) |
subtype3 | 43 | 30.3 (18.5) |
P value = 0.631 (Fisher's exact test), Q value = 0.7
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 137 | 12 | 2 | 7 |
subtype1 | 44 | 6 | 0 | 2 |
subtype2 | 33 | 3 | 0 | 1 |
subtype3 | 60 | 3 | 2 | 4 |
P value = 0.205 (Kruskal-Wallis (anova)), Q value = 0.29
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 2.5 (3.4) |
subtype1 | 50 | 2.7 (3.1) |
subtype2 | 34 | 2.8 (4.9) |
subtype3 | 50 | 2.1 (2.5) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 46 | 5 | 114 |
subtype1 | 4 | 0 | 46 |
subtype2 | 4 | 1 | 38 |
subtype3 | 38 | 4 | 30 |
P value = 0.844 (Fisher's exact test), Q value = 0.87
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 6 | 88 |
subtype1 | 2 | 21 |
subtype2 | 1 | 15 |
subtype3 | 3 | 52 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 77 | 32 | 76 |
P value = 0.385 (logrank test), Q value = 0.49
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 184 | 77 | 0.1 - 122.1 (13.2) |
subtype1 | 77 | 40 | 0.4 - 122.1 (13.9) |
subtype2 | 32 | 10 | 0.8 - 83.2 (13.9) |
subtype3 | 75 | 27 | 0.1 - 68.0 (12.7) |
P value = 3.09e-05 (Kruskal-Wallis (anova)), Q value = 0.00014
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 185 | 62.5 (11.9) |
subtype1 | 77 | 65.9 (11.7) |
subtype2 | 32 | 64.8 (13.6) |
subtype3 | 76 | 58.0 (9.9) |
P value = 8e-05 (Fisher's exact test), Q value = 0.00033
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 8 | 5 | 6 | 1 | 47 | 31 | 26 | 14 | 9 | 7 | 5 | 4 |
subtype1 | 8 | 2 | 2 | 0 | 4 | 15 | 14 | 3 | 4 | 4 | 2 | 2 |
subtype2 | 0 | 1 | 2 | 0 | 10 | 6 | 3 | 5 | 0 | 1 | 0 | 1 |
subtype3 | 0 | 2 | 2 | 1 | 33 | 10 | 9 | 6 | 5 | 2 | 3 | 1 |
P value = 2e-05 (Fisher's exact test), Q value = 9.4e-05
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 32 | 43 | 88 | 5 |
subtype1 | 23 | 7 | 34 | 0 |
subtype2 | 2 | 9 | 17 | 2 |
subtype3 | 7 | 27 | 37 | 3 |
P value = 0.137 (Fisher's exact test), Q value = 0.22
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 77 | 69 | 12 | 8 |
subtype1 | 21 | 35 | 4 | 4 |
subtype2 | 15 | 10 | 2 | 1 |
subtype3 | 41 | 24 | 6 | 3 |
P value = 0.815 (Fisher's exact test), Q value = 0.85
nPatients | 0 | 1 |
---|---|---|
ALL | 136 | 9 |
subtype1 | 46 | 4 |
subtype2 | 25 | 1 |
subtype3 | 65 | 4 |
P value = 0.601 (Fisher's exact test), Q value = 0.68
nPatients | FEMALE | MALE |
---|---|---|
ALL | 27 | 158 |
subtype1 | 9 | 68 |
subtype2 | 5 | 27 |
subtype3 | 13 | 63 |
P value = 0.0103 (Fisher's exact test), Q value = 0.027
nPatients | NO | YES |
---|---|---|
ALL | 125 | 42 |
subtype1 | 58 | 9 |
subtype2 | 21 | 8 |
subtype3 | 46 | 25 |
P value = 0.126 (Kruskal-Wallis (anova)), Q value = 0.21
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 68 | 73.8 (16.2) |
subtype1 | 6 | 85.0 (12.2) |
subtype2 | 14 | 71.4 (17.5) |
subtype3 | 48 | 73.1 (16.0) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | ESOPHAGUS ADENOCARCINOMA NOS | ESOPHAGUS SQUAMOUS CELL CARCINOMA |
---|---|---|
ALL | 89 | 96 |
subtype1 | 77 | 0 |
subtype2 | 11 | 21 |
subtype3 | 1 | 75 |
P value = 0.0432 (Kruskal-Wallis (anova)), Q value = 0.095
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 98 | 34.5 (21.5) |
subtype1 | 38 | 41.4 (24.2) |
subtype2 | 17 | 33.4 (20.9) |
subtype3 | 43 | 28.8 (17.7) |
P value = 0.78 (Fisher's exact test), Q value = 0.82
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 137 | 13 | 2 | 7 |
subtype1 | 52 | 7 | 0 | 2 |
subtype2 | 24 | 1 | 0 | 1 |
subtype3 | 61 | 5 | 2 | 4 |
P value = 0.531 (Kruskal-Wallis (anova)), Q value = 0.62
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 135 | 2.5 (3.4) |
subtype1 | 64 | 2.8 (3.5) |
subtype2 | 22 | 2.5 (4.7) |
subtype3 | 49 | 2.2 (2.6) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 46 | 5 | 114 |
subtype1 | 1 | 0 | 62 |
subtype2 | 8 | 0 | 22 |
subtype3 | 37 | 5 | 30 |
P value = 0.216 (Fisher's exact test), Q value = 0.3
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 6 | 88 |
subtype1 | 3 | 20 |
subtype2 | 0 | 19 |
subtype3 | 3 | 49 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 26 | 28 | 30 | 34 | 8 |
P value = 0.186 (logrank test), Q value = 0.27
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 125 | 44 | 0.1 - 122.1 (13.2) |
subtype1 | 26 | 13 | 2.1 - 46.1 (12.8) |
subtype2 | 28 | 7 | 0.5 - 122.1 (13.7) |
subtype3 | 30 | 11 | 0.3 - 52.6 (12.8) |
subtype4 | 33 | 9 | 0.1 - 68.0 (12.7) |
subtype5 | 8 | 4 | 4.5 - 46.2 (25.1) |
P value = 0.0149 (Kruskal-Wallis (anova)), Q value = 0.038
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 126 | 62.7 (11.5) |
subtype1 | 26 | 68.0 (10.6) |
subtype2 | 28 | 63.2 (11.5) |
subtype3 | 30 | 63.1 (10.1) |
subtype4 | 34 | 58.1 (12.0) |
subtype5 | 8 | 62.2 (11.2) |
P value = 0.0309 (Fisher's exact test), Q value = 0.07
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 | 6 | 3 | 4 | 1 | 42 | 23 | 17 | 12 | 7 | 2 | 3 | 1 |
subtype1 | 3 | 2 | 1 | 0 | 3 | 5 | 4 | 3 | 2 | 1 | 0 | 1 |
subtype2 | 3 | 0 | 1 | 1 | 9 | 5 | 2 | 4 | 0 | 1 | 0 | 0 |
subtype3 | 0 | 1 | 1 | 0 | 6 | 7 | 6 | 2 | 3 | 0 | 2 | 0 |
subtype4 | 0 | 0 | 1 | 0 | 21 | 4 | 5 | 2 | 1 | 0 | 0 | 0 |
subtype5 | 0 | 0 | 0 | 0 | 3 | 2 | 0 | 1 | 1 | 0 | 1 | 0 |
P value = 0.00278 (Fisher's exact test), Q value = 0.0085
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 18 | 35 | 69 | 2 |
subtype1 | 9 | 4 | 13 | 0 |
subtype2 | 4 | 10 | 13 | 0 |
subtype3 | 4 | 4 | 20 | 1 |
subtype4 | 0 | 16 | 17 | 1 |
subtype5 | 1 | 1 | 6 | 0 |
P value = 0.283 (Fisher's exact test), Q value = 0.38
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 62 | 49 | 9 | 3 |
subtype1 | 9 | 13 | 3 | 1 |
subtype2 | 14 | 10 | 1 | 1 |
subtype3 | 12 | 13 | 3 | 1 |
subtype4 | 24 | 9 | 1 | 0 |
subtype5 | 3 | 4 | 1 | 0 |
P value = 0.0812 (Fisher's exact test), Q value = 0.15
nPatients | 0 | 1 |
---|---|---|
ALL | 105 | 4 |
subtype1 | 18 | 1 |
subtype2 | 25 | 0 |
subtype3 | 25 | 2 |
subtype4 | 32 | 0 |
subtype5 | 5 | 1 |
P value = 0.647 (Fisher's exact test), Q value = 0.71
nPatients | FEMALE | MALE |
---|---|---|
ALL | 18 | 108 |
subtype1 | 4 | 22 |
subtype2 | 6 | 22 |
subtype3 | 3 | 27 |
subtype4 | 5 | 29 |
subtype5 | 0 | 8 |
P value = 0.628 (Fisher's exact test), Q value = 0.7
nPatients | NO | YES |
---|---|---|
ALL | 85 | 31 |
subtype1 | 19 | 4 |
subtype2 | 19 | 6 |
subtype3 | 21 | 7 |
subtype4 | 21 | 11 |
subtype5 | 5 | 3 |
P value = 0.39 (Kruskal-Wallis (anova)), Q value = 0.49
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 48 | 69.2 (16.2) |
subtype1 | 4 | 60.0 (28.3) |
subtype2 | 7 | 72.9 (19.8) |
subtype3 | 11 | 69.1 (14.5) |
subtype4 | 21 | 67.1 (13.5) |
subtype5 | 5 | 80.0 (14.1) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | ESOPHAGUS ADENOCARCINOMA NOS | ESOPHAGUS SQUAMOUS CELL CARCINOMA |
---|---|---|
ALL | 48 | 78 |
subtype1 | 22 | 4 |
subtype2 | 12 | 16 |
subtype3 | 10 | 20 |
subtype4 | 1 | 33 |
subtype5 | 3 | 5 |
P value = 0.395 (Kruskal-Wallis (anova)), Q value = 0.49
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 66 | 36.4 (20.6) |
subtype1 | 11 | 34.7 (17.0) |
subtype2 | 13 | 32.5 (19.2) |
subtype3 | 17 | 48.0 (27.9) |
subtype4 | 21 | 30.2 (14.1) |
subtype5 | 4 | 37.2 (12.8) |
P value = 0.0712 (Fisher's exact test), Q value = 0.14
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 101 | 10 | 1 | 7 |
subtype1 | 20 | 3 | 0 | 3 |
subtype2 | 27 | 0 | 0 | 0 |
subtype3 | 20 | 4 | 0 | 2 |
subtype4 | 29 | 2 | 0 | 2 |
subtype5 | 5 | 1 | 1 | 0 |
P value = 0.412 (Kruskal-Wallis (anova)), Q value = 0.5
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 97 | 2.2 (2.8) |
subtype1 | 24 | 2.8 (3.3) |
subtype2 | 20 | 1.8 (2.5) |
subtype3 | 27 | 2.1 (3.0) |
subtype4 | 19 | 1.6 (2.2) |
subtype5 | 7 | 2.9 (2.3) |
P value = 0.00038 (Fisher's exact test), Q value = 0.0014
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 43 | 2 | 73 |
subtype1 | 2 | 0 | 20 |
subtype2 | 7 | 1 | 18 |
subtype3 | 11 | 0 | 18 |
subtype4 | 21 | 0 | 12 |
subtype5 | 2 | 1 | 5 |
P value = 0.198 (Fisher's exact test), Q value = 0.29
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 2 | 68 |
subtype1 | 0 | 7 |
subtype2 | 0 | 14 |
subtype3 | 0 | 19 |
subtype4 | 1 | 25 |
subtype5 | 1 | 3 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 23 | 21 | 22 | 26 | 34 |
P value = 0.421 (logrank test), Q value = 0.51
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 125 | 44 | 0.1 - 122.1 (13.2) |
subtype1 | 23 | 11 | 1.4 - 46.2 (18.4) |
subtype2 | 21 | 6 | 0.5 - 122.1 (15.5) |
subtype3 | 22 | 10 | 2.7 - 52.6 (13.0) |
subtype4 | 25 | 7 | 0.3 - 52.3 (12.6) |
subtype5 | 34 | 10 | 0.1 - 68.0 (12.9) |
P value = 0.000524 (Kruskal-Wallis (anova)), Q value = 0.0019
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 126 | 62.7 (11.5) |
subtype1 | 23 | 71.4 (9.4) |
subtype2 | 21 | 64.0 (10.6) |
subtype3 | 22 | 62.8 (10.0) |
subtype4 | 26 | 58.1 (11.6) |
subtype5 | 34 | 59.5 (11.2) |
P value = 0.00946 (Fisher's exact test), Q value = 0.025
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 | 6 | 3 | 4 | 1 | 42 | 23 | 17 | 12 | 7 | 2 | 3 | 1 |
subtype1 | 3 | 2 | 1 | 0 | 1 | 5 | 3 | 2 | 2 | 2 | 0 | 0 |
subtype2 | 3 | 0 | 1 | 0 | 6 | 5 | 2 | 2 | 0 | 0 | 0 | 0 |
subtype3 | 0 | 0 | 0 | 0 | 4 | 5 | 4 | 3 | 2 | 0 | 2 | 1 |
subtype4 | 0 | 0 | 1 | 1 | 12 | 3 | 6 | 2 | 1 | 0 | 0 | 0 |
subtype5 | 0 | 1 | 1 | 0 | 19 | 5 | 2 | 3 | 2 | 0 | 1 | 0 |
P value = 0.00317 (Fisher's exact test), Q value = 0.0095
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 18 | 35 | 69 | 2 |
subtype1 | 9 | 3 | 10 | 0 |
subtype2 | 4 | 7 | 9 | 0 |
subtype3 | 3 | 3 | 15 | 1 |
subtype4 | 0 | 8 | 18 | 0 |
subtype5 | 2 | 14 | 17 | 1 |
P value = 0.06 (Fisher's exact test), Q value = 0.12
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 62 | 49 | 9 | 3 |
subtype1 | 6 | 10 | 4 | 2 |
subtype2 | 11 | 9 | 0 | 0 |
subtype3 | 8 | 11 | 2 | 1 |
subtype4 | 14 | 10 | 1 | 0 |
subtype5 | 23 | 9 | 2 | 0 |
P value = 0.0521 (Fisher's exact test), Q value = 0.11
nPatients | 0 | 1 |
---|---|---|
ALL | 105 | 4 |
subtype1 | 13 | 0 |
subtype2 | 20 | 0 |
subtype3 | 16 | 3 |
subtype4 | 26 | 0 |
subtype5 | 30 | 1 |
P value = 0.132 (Fisher's exact test), Q value = 0.22
nPatients | FEMALE | MALE |
---|---|---|
ALL | 18 | 108 |
subtype1 | 4 | 19 |
subtype2 | 5 | 16 |
subtype3 | 1 | 21 |
subtype4 | 1 | 25 |
subtype5 | 7 | 27 |
P value = 0.142 (Fisher's exact test), Q value = 0.22
nPatients | NO | YES |
---|---|---|
ALL | 85 | 31 |
subtype1 | 19 | 2 |
subtype2 | 15 | 4 |
subtype3 | 13 | 8 |
subtype4 | 14 | 9 |
subtype5 | 24 | 8 |
P value = 0.0874 (Kruskal-Wallis (anova)), Q value = 0.16
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 48 | 69.2 (16.2) |
subtype1 | 1 | 90.0 (NA) |
subtype2 | 5 | 82.0 (13.0) |
subtype3 | 6 | 66.7 (17.5) |
subtype4 | 15 | 63.3 (15.4) |
subtype5 | 21 | 70.0 (15.8) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | ESOPHAGUS ADENOCARCINOMA NOS | ESOPHAGUS SQUAMOUS CELL CARCINOMA |
---|---|---|
ALL | 48 | 78 |
subtype1 | 23 | 0 |
subtype2 | 10 | 11 |
subtype3 | 12 | 10 |
subtype4 | 2 | 24 |
subtype5 | 1 | 33 |
P value = 0.318 (Kruskal-Wallis (anova)), Q value = 0.41
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 66 | 36.4 (20.6) |
subtype1 | 11 | 37.2 (20.2) |
subtype2 | 9 | 34.3 (20.9) |
subtype3 | 14 | 45.5 (21.2) |
subtype4 | 16 | 32.8 (24.8) |
subtype5 | 16 | 32.6 (14.9) |
P value = 0.152 (Fisher's exact test), Q value = 0.23
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 101 | 10 | 1 | 7 |
subtype1 | 18 | 2 | 0 | 2 |
subtype2 | 20 | 0 | 0 | 0 |
subtype3 | 14 | 4 | 0 | 1 |
subtype4 | 24 | 1 | 0 | 0 |
subtype5 | 25 | 3 | 1 | 4 |
P value = 0.0309 (Kruskal-Wallis (anova)), Q value = 0.07
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 97 | 2.2 (2.8) |
subtype1 | 23 | 3.9 (4.0) |
subtype2 | 18 | 1.2 (1.8) |
subtype3 | 21 | 1.9 (2.3) |
subtype4 | 12 | 2.5 (2.4) |
subtype5 | 23 | 1.3 (1.8) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 43 | 2 | 73 |
subtype1 | 0 | 0 | 19 |
subtype2 | 3 | 1 | 15 |
subtype3 | 6 | 0 | 15 |
subtype4 | 18 | 0 | 7 |
subtype5 | 16 | 1 | 17 |
P value = 0.774 (Fisher's exact test), Q value = 0.82
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 2 | 68 |
subtype1 | 0 | 4 |
subtype2 | 0 | 9 |
subtype3 | 0 | 10 |
subtype4 | 0 | 21 |
subtype5 | 2 | 24 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 82 | 69 | 22 | 11 |
P value = 0.859 (logrank test), Q value = 0.87
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 183 | 77 | 0.1 - 122.1 (13.2) |
subtype1 | 82 | 42 | 0.4 - 122.1 (13.4) |
subtype2 | 68 | 21 | 0.1 - 68.0 (12.6) |
subtype3 | 22 | 10 | 1.3 - 54.0 (17.2) |
subtype4 | 11 | 4 | 2.6 - 31.6 (14.9) |
P value = 5.44e-06 (Kruskal-Wallis (anova)), Q value = 5.4e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 184 | 62.5 (11.9) |
subtype1 | 82 | 67.1 (11.8) |
subtype2 | 69 | 57.9 (10.6) |
subtype3 | 22 | 61.1 (11.9) |
subtype4 | 11 | 59.0 (8.0) |
P value = 5e-05 (Fisher's exact test), Q value = 0.00022
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 8 | 5 | 6 | 1 | 46 | 31 | 26 | 14 | 9 | 7 | 5 | 4 |
subtype1 | 8 | 2 | 1 | 0 | 5 | 16 | 14 | 4 | 4 | 4 | 2 | 3 |
subtype2 | 0 | 1 | 4 | 1 | 32 | 8 | 10 | 5 | 2 | 2 | 3 | 0 |
subtype3 | 0 | 2 | 1 | 0 | 5 | 5 | 2 | 2 | 2 | 0 | 0 | 1 |
subtype4 | 0 | 0 | 0 | 0 | 4 | 2 | 0 | 3 | 1 | 1 | 0 | 0 |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 32 | 42 | 88 | 5 |
subtype1 | 24 | 8 | 36 | 0 |
subtype2 | 3 | 24 | 38 | 3 |
subtype3 | 5 | 7 | 8 | 0 |
subtype4 | 0 | 3 | 6 | 2 |
P value = 0.00232 (Fisher's exact test), Q value = 0.0072
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 76 | 69 | 12 | 8 |
subtype1 | 21 | 37 | 6 | 4 |
subtype2 | 42 | 19 | 3 | 3 |
subtype3 | 6 | 12 | 2 | 0 |
subtype4 | 7 | 1 | 1 | 1 |
P value = 0.775 (Fisher's exact test), Q value = 0.82
nPatients | 0 | 1 |
---|---|---|
ALL | 135 | 9 |
subtype1 | 47 | 5 |
subtype2 | 59 | 3 |
subtype3 | 19 | 1 |
subtype4 | 10 | 0 |
P value = 0.64 (Fisher's exact test), Q value = 0.71
nPatients | FEMALE | MALE |
---|---|---|
ALL | 26 | 158 |
subtype1 | 11 | 71 |
subtype2 | 9 | 60 |
subtype3 | 3 | 19 |
subtype4 | 3 | 8 |
P value = 0.00015 (Fisher's exact test), Q value = 0.00059
nPatients | NO | YES |
---|---|---|
ALL | 124 | 42 |
subtype1 | 63 | 7 |
subtype2 | 41 | 24 |
subtype3 | 16 | 5 |
subtype4 | 4 | 6 |
P value = 0.029 (Kruskal-Wallis (anova)), Q value = 0.068
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 67 | 73.6 (16.2) |
subtype1 | 6 | 85.0 (12.2) |
subtype2 | 45 | 70.4 (15.9) |
subtype3 | 10 | 82.0 (14.0) |
subtype4 | 6 | 71.7 (18.3) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | ESOPHAGUS ADENOCARCINOMA NOS | ESOPHAGUS SQUAMOUS CELL CARCINOMA |
---|---|---|
ALL | 89 | 95 |
subtype1 | 82 | 0 |
subtype2 | 1 | 68 |
subtype3 | 3 | 19 |
subtype4 | 3 | 8 |
P value = 0.0772 (Kruskal-Wallis (anova)), Q value = 0.15
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 97 | 34.7 (21.5) |
subtype1 | 38 | 41.3 (24.5) |
subtype2 | 39 | 30.4 (19.3) |
subtype3 | 16 | 28.0 (16.6) |
subtype4 | 4 | 40.9 (14.1) |
P value = 0.85 (Fisher's exact test), Q value = 0.87
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 136 | 13 | 2 | 7 |
subtype1 | 55 | 7 | 0 | 3 |
subtype2 | 55 | 4 | 2 | 4 |
subtype3 | 18 | 1 | 0 | 0 |
subtype4 | 8 | 1 | 0 | 0 |
P value = 0.166 (Kruskal-Wallis (anova)), Q value = 0.25
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 2.5 (3.4) |
subtype1 | 67 | 3.0 (3.9) |
subtype2 | 43 | 1.7 (2.4) |
subtype3 | 17 | 2.6 (2.5) |
subtype4 | 7 | 2.9 (5.2) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 46 | 5 | 113 |
subtype1 | 1 | 0 | 65 |
subtype2 | 37 | 2 | 27 |
subtype3 | 4 | 3 | 14 |
subtype4 | 4 | 0 | 7 |
P value = 0.0202 (Fisher's exact test), Q value = 0.05
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 5 | 88 |
subtype1 | 3 | 21 |
subtype2 | 0 | 49 |
subtype3 | 2 | 9 |
subtype4 | 0 | 9 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 68 | 20 | 96 |
P value = 0.837 (logrank test), Q value = 0.87
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 183 | 77 | 0.1 - 122.1 (13.2) |
subtype1 | 68 | 34 | 1.4 - 122.1 (15.3) |
subtype2 | 20 | 10 | 0.4 - 54.0 (10.9) |
subtype3 | 95 | 33 | 0.1 - 68.0 (12.7) |
P value = 6.96e-06 (Kruskal-Wallis (anova)), Q value = 5.4e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 184 | 62.5 (11.9) |
subtype1 | 68 | 67.1 (11.7) |
subtype2 | 20 | 65.5 (13.3) |
subtype3 | 96 | 58.6 (10.5) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 8 | 5 | 6 | 1 | 46 | 31 | 26 | 14 | 9 | 7 | 5 | 4 |
subtype1 | 6 | 2 | 1 | 0 | 3 | 16 | 13 | 4 | 1 | 5 | 2 | 3 |
subtype2 | 2 | 0 | 1 | 0 | 2 | 2 | 1 | 1 | 3 | 0 | 0 | 0 |
subtype3 | 0 | 3 | 4 | 1 | 41 | 13 | 12 | 9 | 5 | 2 | 3 | 1 |
P value = 0.00193 (Fisher's exact test), Q value = 0.0064
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 32 | 42 | 88 | 5 |
subtype1 | 18 | 9 | 30 | 1 |
subtype2 | 6 | 2 | 7 | 0 |
subtype3 | 8 | 31 | 51 | 4 |
P value = 0.00496 (Fisher's exact test), Q value = 0.014
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 76 | 69 | 12 | 8 |
subtype1 | 17 | 32 | 3 | 5 |
subtype2 | 5 | 7 | 3 | 0 |
subtype3 | 54 | 30 | 6 | 3 |
P value = 0.342 (Fisher's exact test), Q value = 0.44
nPatients | 0 | 1 |
---|---|---|
ALL | 135 | 9 |
subtype1 | 42 | 5 |
subtype2 | 9 | 0 |
subtype3 | 84 | 4 |
P value = 0.912 (Fisher's exact test), Q value = 0.91
nPatients | FEMALE | MALE |
---|---|---|
ALL | 26 | 158 |
subtype1 | 10 | 58 |
subtype2 | 2 | 18 |
subtype3 | 14 | 82 |
P value = 0.00027 (Fisher's exact test), Q value = 0.001
nPatients | NO | YES |
---|---|---|
ALL | 124 | 42 |
subtype1 | 48 | 9 |
subtype2 | 19 | 0 |
subtype3 | 57 | 33 |
P value = 0.0361 (Kruskal-Wallis (anova)), Q value = 0.081
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 67 | 73.6 (16.2) |
subtype1 | 6 | 85.0 (12.2) |
subtype2 | 1 | 90.0 (NA) |
subtype3 | 60 | 72.2 (16.2) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | ESOPHAGUS ADENOCARCINOMA NOS | ESOPHAGUS SQUAMOUS CELL CARCINOMA |
---|---|---|
ALL | 89 | 95 |
subtype1 | 68 | 0 |
subtype2 | 20 | 0 |
subtype3 | 1 | 95 |
P value = 0.125 (Kruskal-Wallis (anova)), Q value = 0.21
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 97 | 34.7 (21.5) |
subtype1 | 27 | 37.6 (25.6) |
subtype2 | 14 | 43.8 (21.9) |
subtype3 | 56 | 31.0 (18.6) |
P value = 0.142 (Fisher's exact test), Q value = 0.22
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 136 | 13 | 2 | 7 |
subtype1 | 46 | 8 | 0 | 1 |
subtype2 | 12 | 0 | 0 | 2 |
subtype3 | 78 | 5 | 2 | 4 |
P value = 0.0507 (Kruskal-Wallis (anova)), Q value = 0.11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 2.5 (3.4) |
subtype1 | 56 | 3.5 (4.4) |
subtype2 | 15 | 1.7 (2.1) |
subtype3 | 63 | 1.9 (2.4) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 46 | 5 | 113 |
subtype1 | 1 | 0 | 54 |
subtype2 | 0 | 0 | 17 |
subtype3 | 45 | 5 | 42 |
P value = 0.172 (Fisher's exact test), Q value = 0.26
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 5 | 88 |
subtype1 | 2 | 14 |
subtype2 | 1 | 9 |
subtype3 | 2 | 65 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 85 | 87 | 12 |
P value = 0.603 (logrank test), Q value = 0.68
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 183 | 77 | 0.1 - 122.1 (13.2) |
subtype1 | 85 | 44 | 0.4 - 122.1 (13.9) |
subtype2 | 86 | 31 | 0.1 - 68.0 (12.8) |
subtype3 | 12 | 2 | 0.3 - 25.2 (12.4) |
P value = 1.95e-06 (Kruskal-Wallis (anova)), Q value = 5.4e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 184 | 62.5 (11.9) |
subtype1 | 85 | 66.7 (11.9) |
subtype2 | 87 | 58.0 (10.0) |
subtype3 | 12 | 65.8 (13.3) |
P value = 2e-05 (Fisher's exact test), Q value = 9.4e-05
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 8 | 5 | 6 | 1 | 46 | 31 | 26 | 14 | 9 | 7 | 5 | 4 |
subtype1 | 8 | 2 | 2 | 0 | 5 | 17 | 14 | 3 | 4 | 5 | 2 | 3 |
subtype2 | 0 | 2 | 3 | 1 | 38 | 12 | 11 | 7 | 5 | 2 | 3 | 1 |
subtype3 | 0 | 1 | 1 | 0 | 3 | 2 | 1 | 4 | 0 | 0 | 0 | 0 |
P value = 2e-05 (Fisher's exact test), Q value = 9.4e-05
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 32 | 43 | 87 | 5 |
subtype1 | 24 | 10 | 36 | 0 |
subtype2 | 7 | 30 | 45 | 3 |
subtype3 | 1 | 3 | 6 | 2 |
P value = 0.0561 (Fisher's exact test), Q value = 0.11
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 76 | 69 | 12 | 8 |
subtype1 | 22 | 37 | 6 | 5 |
subtype2 | 48 | 27 | 6 | 3 |
subtype3 | 6 | 5 | 0 | 0 |
P value = 0.632 (Fisher's exact test), Q value = 0.7
nPatients | 0 | 1 |
---|---|---|
ALL | 135 | 9 |
subtype1 | 49 | 5 |
subtype2 | 76 | 4 |
subtype3 | 10 | 0 |
P value = 0.748 (Fisher's exact test), Q value = 0.8
nPatients | FEMALE | MALE |
---|---|---|
ALL | 27 | 157 |
subtype1 | 11 | 74 |
subtype2 | 14 | 73 |
subtype3 | 2 | 10 |
P value = 0.00197 (Fisher's exact test), Q value = 0.0064
nPatients | NO | YES |
---|---|---|
ALL | 125 | 41 |
subtype1 | 64 | 9 |
subtype2 | 54 | 27 |
subtype3 | 7 | 5 |
P value = 0.136 (Kruskal-Wallis (anova)), Q value = 0.22
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 67 | 74.0 (16.2) |
subtype1 | 6 | 85.0 (12.2) |
subtype2 | 55 | 72.9 (16.3) |
subtype3 | 6 | 73.3 (17.5) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | ESOPHAGUS ADENOCARCINOMA NOS | ESOPHAGUS SQUAMOUS CELL CARCINOMA |
---|---|---|
ALL | 89 | 95 |
subtype1 | 85 | 0 |
subtype2 | 1 | 86 |
subtype3 | 3 | 9 |
P value = 0.0198 (Kruskal-Wallis (anova)), Q value = 0.05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 97 | 34.7 (21.5) |
subtype1 | 40 | 40.3 (24.3) |
subtype2 | 50 | 28.3 (15.9) |
subtype3 | 7 | 48.1 (27.4) |
P value = 0.562 (Fisher's exact test), Q value = 0.65
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 136 | 13 | 2 | 7 |
subtype1 | 56 | 8 | 0 | 3 |
subtype2 | 71 | 4 | 2 | 4 |
subtype3 | 9 | 1 | 0 | 0 |
P value = 0.11 (Kruskal-Wallis (anova)), Q value = 0.19
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 135 | 2.5 (3.4) |
subtype1 | 69 | 3.2 (4.1) |
subtype2 | 58 | 2.0 (2.5) |
subtype3 | 8 | 0.9 (0.8) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 45 | 5 | 114 |
subtype1 | 1 | 0 | 68 |
subtype2 | 41 | 5 | 37 |
subtype3 | 3 | 0 | 9 |
P value = 0.396 (Fisher's exact test), Q value = 0.49
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 6 | 87 |
subtype1 | 3 | 22 |
subtype2 | 3 | 57 |
subtype3 | 0 | 8 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 63 | 26 | 62 | 33 |
P value = 0.0174 (logrank test), Q value = 0.044
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 183 | 77 | 0.1 - 122.1 (13.2) |
subtype1 | 63 | 38 | 0.4 - 122.1 (13.5) |
subtype2 | 26 | 7 | 3.0 - 83.2 (19.1) |
subtype3 | 61 | 22 | 0.1 - 35.2 (12.5) |
subtype4 | 33 | 10 | 0.8 - 68.0 (15.5) |
P value = 1.85e-06 (Kruskal-Wallis (anova)), Q value = 5.4e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 184 | 62.5 (11.9) |
subtype1 | 63 | 65.1 (11.9) |
subtype2 | 26 | 71.2 (11.5) |
subtype3 | 62 | 58.1 (11.1) |
subtype4 | 33 | 59.3 (8.6) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 8 | 5 | 6 | 1 | 46 | 31 | 26 | 14 | 9 | 7 | 5 | 4 |
subtype1 | 7 | 2 | 2 | 0 | 1 | 11 | 12 | 2 | 3 | 3 | 1 | 3 |
subtype2 | 1 | 0 | 0 | 0 | 4 | 7 | 3 | 3 | 1 | 2 | 1 | 0 |
subtype3 | 0 | 2 | 2 | 1 | 24 | 9 | 9 | 6 | 4 | 2 | 1 | 0 |
subtype4 | 0 | 1 | 2 | 0 | 17 | 4 | 2 | 3 | 1 | 0 | 2 | 1 |
P value = 0.00083 (Fisher's exact test), Q value = 0.0029
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 32 | 43 | 87 | 5 |
subtype1 | 19 | 8 | 23 | 0 |
subtype2 | 5 | 3 | 15 | 1 |
subtype3 | 4 | 21 | 31 | 4 |
subtype4 | 4 | 11 | 18 | 0 |
P value = 0.0438 (Fisher's exact test), Q value = 0.095
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 76 | 69 | 12 | 8 |
subtype1 | 14 | 29 | 4 | 3 |
subtype2 | 8 | 11 | 2 | 2 |
subtype3 | 33 | 19 | 5 | 2 |
subtype4 | 21 | 10 | 1 | 1 |
P value = 0.203 (Fisher's exact test), Q value = 0.29
nPatients | 0 | 1 |
---|---|---|
ALL | 135 | 9 |
subtype1 | 33 | 4 |
subtype2 | 19 | 1 |
subtype3 | 55 | 1 |
subtype4 | 28 | 3 |
P value = 0.484 (Fisher's exact test), Q value = 0.57
nPatients | FEMALE | MALE |
---|---|---|
ALL | 27 | 157 |
subtype1 | 7 | 56 |
subtype2 | 5 | 21 |
subtype3 | 8 | 54 |
subtype4 | 7 | 26 |
P value = 0.00215 (Fisher's exact test), Q value = 0.0069
nPatients | NO | YES |
---|---|---|
ALL | 125 | 41 |
subtype1 | 49 | 6 |
subtype2 | 19 | 3 |
subtype3 | 35 | 23 |
subtype4 | 22 | 9 |
P value = 0.116 (Kruskal-Wallis (anova)), Q value = 0.2
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 67 | 74.0 (16.2) |
subtype1 | 6 | 85.0 (12.2) |
subtype2 | 1 | 90.0 (NA) |
subtype3 | 37 | 72.4 (15.5) |
subtype4 | 23 | 73.0 (17.7) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | ESOPHAGUS ADENOCARCINOMA NOS | ESOPHAGUS SQUAMOUS CELL CARCINOMA |
---|---|---|
ALL | 89 | 95 |
subtype1 | 63 | 0 |
subtype2 | 26 | 0 |
subtype3 | 0 | 62 |
subtype4 | 0 | 33 |
P value = 0.136 (Kruskal-Wallis (anova)), Q value = 0.22
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 97 | 34.7 (21.5) |
subtype1 | 28 | 35.7 (20.2) |
subtype2 | 13 | 48.5 (30.4) |
subtype3 | 35 | 33.3 (19.0) |
subtype4 | 21 | 27.1 (17.7) |
P value = 0.676 (Fisher's exact test), Q value = 0.73
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 136 | 13 | 2 | 7 |
subtype1 | 41 | 5 | 0 | 1 |
subtype2 | 18 | 3 | 0 | 2 |
subtype3 | 48 | 3 | 2 | 2 |
subtype4 | 29 | 2 | 0 | 2 |
P value = 0.21 (Kruskal-Wallis (anova)), Q value = 0.29
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 135 | 2.5 (3.4) |
subtype1 | 49 | 2.9 (3.3) |
subtype2 | 23 | 3.5 (5.4) |
subtype3 | 40 | 1.8 (2.2) |
subtype4 | 23 | 2.0 (2.8) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 45 | 5 | 114 |
subtype1 | 1 | 0 | 49 |
subtype2 | 0 | 0 | 22 |
subtype3 | 30 | 4 | 26 |
subtype4 | 14 | 1 | 17 |
P value = 0.176 (Fisher's exact test), Q value = 0.26
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 6 | 87 |
subtype1 | 3 | 17 |
subtype2 | 0 | 6 |
subtype3 | 1 | 46 |
subtype4 | 2 | 18 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 67 | 66 | 35 | 11 |
P value = 0.313 (logrank test), Q value = 0.41
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 178 | 77 | 0.1 - 122.1 (13.2) |
subtype1 | 67 | 36 | 0.4 - 122.1 (13.5) |
subtype2 | 65 | 25 | 0.1 - 52.3 (12.8) |
subtype3 | 35 | 11 | 0.3 - 83.2 (15.5) |
subtype4 | 11 | 5 | 0.8 - 68.0 (9.3) |
P value = 1.86e-05 (Kruskal-Wallis (anova)), Q value = 9.4e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 179 | 62.5 (12.0) |
subtype1 | 67 | 66.3 (12.5) |
subtype2 | 66 | 57.1 (9.9) |
subtype3 | 35 | 66.0 (12.1) |
subtype4 | 11 | 61.6 (8.2) |
P value = 0.00012 (Fisher's exact test), Q value = 0.00049
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 | 5 | 5 | 1 | 46 | 30 | 25 | 14 | 9 | 7 | 5 | 4 |
subtype1 | 7 | 2 | 2 | 0 | 2 | 12 | 12 | 3 | 3 | 2 | 2 | 3 |
subtype2 | 0 | 2 | 2 | 1 | 30 | 8 | 8 | 2 | 5 | 2 | 3 | 1 |
subtype3 | 0 | 1 | 1 | 0 | 12 | 8 | 4 | 6 | 1 | 2 | 0 | 0 |
subtype4 | 0 | 0 | 0 | 0 | 2 | 2 | 1 | 3 | 0 | 1 | 0 | 0 |
P value = 0.00171 (Fisher's exact test), Q value = 0.0058
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 31 | 42 | 85 | 5 |
subtype1 | 20 | 8 | 27 | 0 |
subtype2 | 7 | 22 | 34 | 1 |
subtype3 | 4 | 9 | 19 | 3 |
subtype4 | 0 | 3 | 5 | 1 |
P value = 0.0958 (Fisher's exact test), Q value = 0.17
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 73 | 68 | 12 | 8 |
subtype1 | 16 | 32 | 5 | 2 |
subtype2 | 35 | 20 | 5 | 3 |
subtype3 | 18 | 13 | 1 | 2 |
subtype4 | 4 | 3 | 1 | 1 |
P value = 0.213 (Fisher's exact test), Q value = 0.29
nPatients | 0 | 1 |
---|---|---|
ALL | 132 | 9 |
subtype1 | 36 | 5 |
subtype2 | 56 | 4 |
subtype3 | 32 | 0 |
subtype4 | 8 | 0 |
P value = 0.911 (Fisher's exact test), Q value = 0.91
nPatients | FEMALE | MALE |
---|---|---|
ALL | 25 | 154 |
subtype1 | 10 | 57 |
subtype2 | 9 | 57 |
subtype3 | 4 | 31 |
subtype4 | 2 | 9 |
P value = 0.00359 (Fisher's exact test), Q value = 0.01
nPatients | NO | YES |
---|---|---|
ALL | 123 | 39 |
subtype1 | 53 | 6 |
subtype2 | 41 | 21 |
subtype3 | 20 | 11 |
subtype4 | 9 | 1 |
P value = 0.0578 (Kruskal-Wallis (anova)), Q value = 0.11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 65 | 74.2 (16.4) |
subtype1 | 6 | 85.0 (12.2) |
subtype2 | 41 | 71.7 (16.6) |
subtype3 | 13 | 72.3 (17.4) |
subtype4 | 5 | 86.0 (5.5) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | ESOPHAGUS ADENOCARCINOMA NOS | ESOPHAGUS SQUAMOUS CELL CARCINOMA |
---|---|---|
ALL | 87 | 92 |
subtype1 | 67 | 0 |
subtype2 | 1 | 65 |
subtype3 | 15 | 20 |
subtype4 | 4 | 7 |
P value = 0.0226 (Kruskal-Wallis (anova)), Q value = 0.054
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 94 | 35.1 (21.6) |
subtype1 | 32 | 38.0 (20.2) |
subtype2 | 39 | 26.9 (16.3) |
subtype3 | 20 | 45.1 (26.9) |
subtype4 | 3 | 43.3 (30.6) |
P value = 0.312 (Fisher's exact test), Q value = 0.41
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 132 | 13 | 2 | 7 |
subtype1 | 45 | 6 | 0 | 2 |
subtype2 | 55 | 2 | 1 | 3 |
subtype3 | 24 | 5 | 1 | 1 |
subtype4 | 8 | 0 | 0 | 1 |
P value = 0.086 (Kruskal-Wallis (anova)), Q value = 0.16
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 132 | 2.6 (3.4) |
subtype1 | 55 | 2.9 (3.2) |
subtype2 | 40 | 2.5 (2.7) |
subtype3 | 28 | 2.0 (4.6) |
subtype4 | 9 | 2.1 (3.9) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 44 | 4 | 111 |
subtype1 | 1 | 0 | 51 |
subtype2 | 34 | 3 | 25 |
subtype3 | 7 | 1 | 26 |
subtype4 | 2 | 0 | 9 |
P value = 0.447 (Fisher's exact test), Q value = 0.54
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 6 | 84 |
subtype1 | 2 | 17 |
subtype2 | 2 | 45 |
subtype3 | 1 | 16 |
subtype4 | 1 | 6 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 63 | 22 | 94 |
P value = 0.0496 (logrank test), Q value = 0.11
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 178 | 77 | 0.1 - 122.1 (13.2) |
subtype1 | 63 | 39 | 0.4 - 122.1 (13.5) |
subtype2 | 22 | 6 | 3.0 - 83.2 (19.1) |
subtype3 | 93 | 32 | 0.1 - 68.0 (12.8) |
P value = 3.12e-07 (Kruskal-Wallis (anova)), Q value = 4.7e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 179 | 62.5 (12.0) |
subtype1 | 63 | 65.1 (12.3) |
subtype2 | 22 | 72.2 (9.2) |
subtype3 | 94 | 58.6 (10.7) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
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 | 5 | 5 | 1 | 46 | 30 | 25 | 14 | 9 | 7 | 5 | 4 |
subtype1 | 6 | 2 | 2 | 0 | 1 | 12 | 13 | 2 | 3 | 3 | 1 | 3 |
subtype2 | 1 | 0 | 0 | 0 | 4 | 5 | 2 | 2 | 1 | 2 | 1 | 0 |
subtype3 | 0 | 3 | 3 | 1 | 41 | 13 | 10 | 10 | 5 | 2 | 3 | 1 |
P value = 0.00018 (Fisher's exact test), Q value = 0.00069
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 31 | 42 | 85 | 5 |
subtype1 | 19 | 8 | 24 | 0 |
subtype2 | 4 | 2 | 14 | 0 |
subtype3 | 8 | 32 | 47 | 5 |
P value = 0.0065 (Fisher's exact test), Q value = 0.018
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 73 | 68 | 12 | 8 |
subtype1 | 13 | 31 | 4 | 3 |
subtype2 | 8 | 8 | 2 | 2 |
subtype3 | 52 | 29 | 6 | 3 |
P value = 0.463 (Fisher's exact test), Q value = 0.55
nPatients | 0 | 1 |
---|---|---|
ALL | 132 | 9 |
subtype1 | 34 | 4 |
subtype2 | 16 | 1 |
subtype3 | 82 | 4 |
P value = 0.683 (Fisher's exact test), Q value = 0.74
nPatients | FEMALE | MALE |
---|---|---|
ALL | 25 | 154 |
subtype1 | 7 | 56 |
subtype2 | 3 | 19 |
subtype3 | 15 | 79 |
P value = 0.00356 (Fisher's exact test), Q value = 0.01
nPatients | NO | YES |
---|---|---|
ALL | 123 | 39 |
subtype1 | 50 | 6 |
subtype2 | 15 | 3 |
subtype3 | 58 | 30 |
P value = 0.0516 (Kruskal-Wallis (anova)), Q value = 0.11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 65 | 74.2 (16.4) |
subtype1 | 6 | 85.0 (12.2) |
subtype3 | 59 | 73.1 (16.4) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | ESOPHAGUS ADENOCARCINOMA NOS | ESOPHAGUS SQUAMOUS CELL CARCINOMA |
---|---|---|
ALL | 87 | 92 |
subtype1 | 63 | 0 |
subtype2 | 22 | 0 |
subtype3 | 2 | 92 |
P value = 0.021 (Kruskal-Wallis (anova)), Q value = 0.051
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 94 | 35.1 (21.6) |
subtype1 | 28 | 36.1 (19.6) |
subtype2 | 11 | 54.4 (29.4) |
subtype3 | 55 | 30.7 (18.9) |
P value = 0.406 (Fisher's exact test), Q value = 0.5
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 132 | 13 | 2 | 7 |
subtype1 | 42 | 5 | 0 | 1 |
subtype2 | 15 | 3 | 0 | 2 |
subtype3 | 75 | 5 | 2 | 4 |
P value = 0.0788 (Kruskal-Wallis (anova)), Q value = 0.15
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 132 | 2.6 (3.4) |
subtype1 | 50 | 3.0 (3.3) |
subtype2 | 20 | 3.5 (5.7) |
subtype3 | 62 | 1.9 (2.4) |
P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 44 | 4 | 111 |
subtype1 | 1 | 0 | 47 |
subtype2 | 0 | 0 | 20 |
subtype3 | 43 | 4 | 44 |
P value = 0.2 (Fisher's exact test), Q value = 0.29
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 6 | 84 |
subtype1 | 3 | 16 |
subtype2 | 0 | 5 |
subtype3 | 3 | 63 |
-
Cluster data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/ESCA-TP/20125286/ESCA-TP.mergedcluster.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ESCA-TP/19775149/ESCA-TP.merged_data.txt
-
Number of patients = 185
-
Number of clustering approaches = 10
-
Number of selected clinical features = 15
-
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.