This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 12 different clustering approaches and 12 clinical features across 1097 patients, 82 significant findings detected with P value < 0.05 and Q value < 0.25.
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CNMF clustering analysis on array-based mRNA expression data identified 3 subtypes that correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.
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Consensus hierarchical clustering analysis on array-based mRNA expression data identified 3 subtypes that correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'NUMBER_OF_LYMPH_NODES', and 'RACE'.
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5 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', 'NUMBER_OF_LYMPH_NODES', and 'RACE'.
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5 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', 'NUMBER_OF_LYMPH_NODES', and 'RACE'.
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CNMF clustering analysis on RPPA data identified 7 subtypes that 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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Consensus hierarchical clustering analysis on RPPA data identified 3 subtypes that correlate to 'YEARS_TO_BIRTH', 'HISTOLOGICAL_TYPE', and 'RACE'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 7 subtypes that correlate to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', 'NUMBER_OF_LYMPH_NODES', and 'RACE'.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 6 subtypes that correlate to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', 'NUMBER_OF_LYMPH_NODES', and 'RACE'.
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6 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
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9 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', 'HISTOLOGICAL_TYPE', 'NUMBER_OF_LYMPH_NODES', and 'RACE'.
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6 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes correlate to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
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3 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'NUMBER_OF_LYMPH_NODES', and 'RACE'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
RADIATION THERAPY |
HISTOLOGICAL TYPE |
NUMBER OF LYMPH NODES |
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 | Fisher's exact test | Kruskal-Wallis (anova) | Fisher's exact test | Fisher's exact test |
mRNA CNMF subtypes |
0.918 (0.944) |
0.0016 (0.00404) |
0.00025 (0.00072) |
1e-05 (4.97e-05) |
0.175 (0.257) |
0.0666 (0.111) |
0.206 (0.28) |
0.753 (0.822) |
1e-05 (4.97e-05) |
0.883 (0.931) |
0.18 (0.257) |
0.559 (0.659) |
mRNA cHierClus subtypes |
0.185 (0.261) |
1.13e-05 (5.43e-05) |
0.0129 (0.0265) |
0.2 (0.278) |
0.00142 (0.00365) |
0.942 (0.962) |
0.223 (0.3) |
0.446 (0.545) |
1e-05 (4.97e-05) |
0.00777 (0.0167) |
0.0163 (0.0318) |
0.695 (0.775) |
Copy Number Ratio CNMF subtypes |
0.407 (0.501) |
0.00308 (0.00705) |
0.0242 (0.0446) |
1e-05 (4.97e-05) |
0.00079 (0.00207) |
0.148 (0.224) |
7e-05 (0.00024) |
0.0588 (0.0996) |
1e-05 (4.97e-05) |
0.0269 (0.0489) |
8e-05 (0.000262) |
0.886 (0.931) |
METHLYATION CNMF |
0.000782 (0.00207) |
4.65e-05 (0.000176) |
0.00251 (0.00593) |
0.00041 (0.00114) |
0.0156 (0.0309) |
0.3 (0.389) |
0.0439 (0.0781) |
0.97 (0.97) |
1e-05 (4.97e-05) |
0.0147 (0.0299) |
2e-05 (8.73e-05) |
0.9 (0.939) |
RPPA CNMF subtypes |
0.00212 (0.00509) |
0.0152 (0.0305) |
2e-05 (8.73e-05) |
3e-05 (0.000123) |
0.00962 (0.0201) |
0.259 (0.342) |
0.18 (0.257) |
0.00175 (0.00434) |
1e-05 (4.97e-05) |
0.0508 (0.0881) |
1e-05 (4.97e-05) |
0.654 (0.753) |
RPPA cHierClus subtypes |
0.101 (0.161) |
0.00203 (0.00495) |
0.0982 (0.159) |
0.205 (0.28) |
0.536 (0.643) |
0.957 (0.97) |
0.0718 (0.119) |
0.177 (0.257) |
1e-05 (4.97e-05) |
0.486 (0.588) |
0.00013 (0.00039) |
0.373 (0.466) |
RNAseq CNMF subtypes |
4.93e-05 (0.00018) |
7.1e-07 (4.97e-05) |
0.00279 (0.00648) |
0.0001 (0.00032) |
1e-05 (4.97e-05) |
0.848 (0.904) |
0.0218 (0.0408) |
0.818 (0.883) |
1e-05 (4.97e-05) |
1.62e-05 (7.52e-05) |
1e-05 (4.97e-05) |
0.366 (0.466) |
RNAseq cHierClus subtypes |
3.31e-06 (4.97e-05) |
1.37e-10 (1.97e-08) |
1e-05 (4.97e-05) |
1e-05 (4.97e-05) |
1e-05 (4.97e-05) |
0.28 (0.366) |
0.0189 (0.0362) |
0.177 (0.257) |
1e-05 (4.97e-05) |
3.56e-05 (0.000142) |
1e-05 (4.97e-05) |
0.548 (0.652) |
MIRSEQ CNMF |
0.607 (0.71) |
0.00513 (0.0114) |
0.00945 (0.02) |
1e-05 (4.97e-05) |
0.256 (0.342) |
0.694 (0.775) |
0.336 (0.432) |
0.914 (0.944) |
1e-05 (4.97e-05) |
0.105 (0.167) |
1e-05 (4.97e-05) |
0.372 (0.466) |
MIRSEQ CHIERARCHICAL |
0.0316 (0.0569) |
6.34e-05 (0.000223) |
3e-05 (0.000123) |
5e-05 (0.00018) |
8e-05 (0.000262) |
0.112 (0.175) |
0.134 (0.208) |
0.738 (0.811) |
1e-05 (4.97e-05) |
0.00337 (0.00759) |
1e-05 (4.97e-05) |
0.18 (0.257) |
MIRseq Mature CNMF subtypes |
0.967 (0.97) |
0.0786 (0.129) |
0.00027 (0.000762) |
4e-05 (0.000156) |
0.00066 (0.00179) |
0.021 (0.0399) |
0.637 (0.74) |
0.138 (0.212) |
1e-05 (4.97e-05) |
0.0528 (0.0905) |
1e-05 (4.97e-05) |
0.675 (0.765) |
MIRseq Mature cHierClus subtypes |
0.201 (0.278) |
0.0465 (0.0816) |
0.00011 (0.000337) |
0.00011 (0.000337) |
0.00022 (0.000647) |
0.712 (0.789) |
0.67 (0.765) |
0.375 (0.466) |
1e-05 (4.97e-05) |
0.00554 (0.0121) |
1e-05 (4.97e-05) |
0.821 (0.883) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 234 | 118 | 174 |
P value = 0.918 (logrank test), Q value = 0.94
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 514 | 83 | 0.2 - 282.9 (33.7) |
subtype1 | 228 | 35 | 0.2 - 281.3 (31.9) |
subtype2 | 117 | 20 | 0.3 - 282.9 (50.7) |
subtype3 | 169 | 28 | 0.2 - 255.7 (32.6) |
P value = 0.0016 (Kruskal-Wallis (anova)), Q value = 0.004
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 520 | 58.1 (13.2) |
subtype1 | 230 | 60.2 (13.1) |
subtype2 | 118 | 55.6 (13.3) |
subtype3 | 172 | 56.9 (13.1) |
P value = 0.00025 (Fisher's exact test), Q value = 0.00072
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 51 | 35 | 3 | 1 | 182 | 113 | 78 | 13 | 19 | 13 | 13 |
subtype1 | 23 | 19 | 3 | 1 | 71 | 55 | 34 | 8 | 2 | 7 | 9 |
subtype2 | 20 | 9 | 0 | 0 | 41 | 20 | 19 | 0 | 5 | 0 | 3 |
subtype3 | 8 | 7 | 0 | 0 | 70 | 38 | 25 | 5 | 12 | 6 | 1 |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 132 | 312 | 60 | 20 |
subtype1 | 64 | 134 | 23 | 12 |
subtype2 | 47 | 51 | 19 | 1 |
subtype3 | 21 | 127 | 18 | 7 |
P value = 0.175 (Fisher's exact test), Q value = 0.26
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 255 | 171 | 60 | 29 |
subtype1 | 108 | 85 | 24 | 9 |
subtype2 | 62 | 38 | 10 | 6 |
subtype3 | 85 | 48 | 26 | 14 |
P value = 0.0666 (Fisher's exact test), Q value = 0.11
nPatients | 0 | 1 |
---|---|---|
ALL | 495 | 15 |
subtype1 | 217 | 8 |
subtype2 | 113 | 0 |
subtype3 | 165 | 7 |
P value = 0.206 (Fisher's exact test), Q value = 0.28
nPatients | FEMALE | MALE |
---|---|---|
ALL | 520 | 6 |
subtype1 | 229 | 5 |
subtype2 | 118 | 0 |
subtype3 | 173 | 1 |
P value = 0.753 (Fisher's exact test), Q value = 0.82
nPatients | NO | YES |
---|---|---|
ALL | 208 | 264 |
subtype1 | 95 | 113 |
subtype2 | 45 | 64 |
subtype3 | 68 | 87 |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER, SPECIFY |
---|---|---|---|---|---|---|
ALL | 446 | 43 | 1 | 12 | 2 | 21 |
subtype1 | 199 | 14 | 0 | 6 | 2 | 13 |
subtype2 | 84 | 24 | 0 | 6 | 0 | 4 |
subtype3 | 163 | 5 | 1 | 0 | 0 | 4 |
P value = 0.883 (Kruskal-Wallis (anova)), Q value = 0.93
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 408 | 1.8 (3.5) |
subtype1 | 166 | 1.6 (2.9) |
subtype2 | 109 | 1.9 (4.2) |
subtype3 | 133 | 2.0 (3.6) |
P value = 0.18 (Fisher's exact test), Q value = 0.26
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 34 | 40 | 361 |
subtype1 | 0 | 13 | 18 | 151 |
subtype2 | 0 | 5 | 7 | 100 |
subtype3 | 1 | 16 | 15 | 110 |
P value = 0.559 (Fisher's exact test), Q value = 0.66
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 7 | 372 |
subtype1 | 4 | 152 |
subtype2 | 2 | 94 |
subtype3 | 1 | 126 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 162 | 272 | 92 |
P value = 0.185 (logrank test), Q value = 0.26
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 514 | 83 | 0.2 - 282.9 (33.7) |
subtype1 | 157 | 23 | 0.3 - 281.3 (33.0) |
subtype2 | 266 | 47 | 0.2 - 212.2 (33.7) |
subtype3 | 91 | 13 | 0.3 - 282.9 (35.3) |
P value = 1.13e-05 (Kruskal-Wallis (anova)), Q value = 5.4e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 520 | 58.1 (13.2) |
subtype1 | 160 | 61.2 (13.4) |
subtype2 | 268 | 57.8 (12.9) |
subtype3 | 92 | 53.4 (12.7) |
P value = 0.0129 (Fisher's exact test), Q value = 0.027
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 51 | 35 | 3 | 1 | 182 | 113 | 78 | 13 | 19 | 13 | 13 |
subtype1 | 17 | 13 | 3 | 1 | 55 | 38 | 19 | 6 | 0 | 3 | 6 |
subtype2 | 25 | 14 | 0 | 0 | 87 | 56 | 51 | 6 | 16 | 8 | 6 |
subtype3 | 9 | 8 | 0 | 0 | 40 | 19 | 8 | 1 | 3 | 2 | 1 |
P value = 0.2 (Fisher's exact test), Q value = 0.28
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 132 | 312 | 60 | 20 |
subtype1 | 47 | 93 | 13 | 8 |
subtype2 | 63 | 159 | 39 | 11 |
subtype3 | 22 | 60 | 8 | 1 |
P value = 0.00142 (Fisher's exact test), Q value = 0.0037
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 255 | 171 | 60 | 29 |
subtype1 | 80 | 62 | 12 | 4 |
subtype2 | 117 | 85 | 42 | 21 |
subtype3 | 58 | 24 | 6 | 4 |
P value = 0.942 (Fisher's exact test), Q value = 0.96
nPatients | 0 | 1 |
---|---|---|
ALL | 495 | 15 |
subtype1 | 151 | 4 |
subtype2 | 256 | 8 |
subtype3 | 88 | 3 |
P value = 0.223 (Fisher's exact test), Q value = 0.3
nPatients | FEMALE | MALE |
---|---|---|
ALL | 520 | 6 |
subtype1 | 158 | 4 |
subtype2 | 270 | 2 |
subtype3 | 92 | 0 |
P value = 0.446 (Fisher's exact test), Q value = 0.54
nPatients | NO | YES |
---|---|---|
ALL | 208 | 264 |
subtype1 | 65 | 81 |
subtype2 | 112 | 132 |
subtype3 | 31 | 51 |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER, SPECIFY |
---|---|---|---|---|---|---|
ALL | 446 | 43 | 1 | 12 | 2 | 21 |
subtype1 | 142 | 5 | 0 | 4 | 2 | 9 |
subtype2 | 220 | 37 | 0 | 8 | 0 | 7 |
subtype3 | 84 | 1 | 1 | 0 | 0 | 5 |
P value = 0.00777 (Kruskal-Wallis (anova)), Q value = 0.017
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 408 | 1.8 (3.5) |
subtype1 | 116 | 1.3 (2.2) |
subtype2 | 206 | 2.2 (4.1) |
subtype3 | 86 | 1.5 (3.3) |
P value = 0.0163 (Fisher's exact test), Q value = 0.032
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 34 | 40 | 361 |
subtype1 | 0 | 10 | 17 | 100 |
subtype2 | 1 | 21 | 11 | 191 |
subtype3 | 0 | 3 | 12 | 70 |
P value = 0.695 (Fisher's exact test), Q value = 0.78
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 7 | 372 |
subtype1 | 1 | 108 |
subtype2 | 5 | 189 |
subtype3 | 1 | 75 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 330 | 131 | 295 | 294 | 29 |
P value = 0.407 (logrank test), Q value = 0.5
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 1065 | 148 | 0.0 - 282.9 (28.2) |
subtype1 | 326 | 38 | 0.2 - 170.2 (26.8) |
subtype2 | 130 | 18 | 0.3 - 129.6 (23.1) |
subtype3 | 289 | 39 | 0.0 - 281.3 (32.9) |
subtype4 | 291 | 48 | 0.0 - 282.9 (25.9) |
subtype5 | 29 | 5 | 6.5 - 127.3 (26.0) |
P value = 0.00308 (Kruskal-Wallis (anova)), Q value = 0.007
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1064 | 58.6 (13.2) |
subtype1 | 323 | 58.9 (13.4) |
subtype2 | 129 | 59.6 (12.5) |
subtype3 | 292 | 59.6 (13.4) |
subtype4 | 292 | 56.5 (12.9) |
subtype5 | 28 | 64.4 (13.3) |
P value = 0.0242 (Fisher's exact test), Q value = 0.045
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 89 | 83 | 6 | 6 | 352 | 253 | 2 | 155 | 27 | 65 | 20 | 13 |
subtype1 | 23 | 27 | 2 | 1 | 102 | 74 | 1 | 62 | 12 | 15 | 6 | 5 |
subtype2 | 9 | 8 | 0 | 1 | 38 | 37 | 0 | 16 | 5 | 12 | 2 | 1 |
subtype3 | 36 | 32 | 4 | 3 | 85 | 64 | 1 | 37 | 4 | 19 | 2 | 5 |
subtype4 | 20 | 15 | 0 | 1 | 116 | 70 | 0 | 38 | 6 | 14 | 9 | 2 |
subtype5 | 1 | 1 | 0 | 0 | 11 | 8 | 0 | 2 | 0 | 5 | 1 | 0 |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 274 | 625 | 137 | 40 |
subtype1 | 85 | 194 | 35 | 15 |
subtype2 | 22 | 83 | 19 | 7 |
subtype3 | 105 | 134 | 49 | 6 |
subtype4 | 54 | 199 | 29 | 11 |
subtype5 | 8 | 15 | 5 | 1 |
P value = 0.00079 (Fisher's exact test), Q value = 0.0021
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 506 | 358 | 119 | 77 |
subtype1 | 136 | 117 | 49 | 19 |
subtype2 | 57 | 44 | 12 | 16 |
subtype3 | 147 | 102 | 18 | 21 |
subtype4 | 156 | 83 | 38 | 16 |
subtype5 | 10 | 12 | 2 | 5 |
P value = 0.148 (Fisher's exact test), Q value = 0.22
nPatients | 0 | 1 |
---|---|---|
ALL | 889 | 22 |
subtype1 | 281 | 7 |
subtype2 | 102 | 2 |
subtype3 | 241 | 2 |
subtype4 | 244 | 10 |
subtype5 | 21 | 1 |
P value = 7e-05 (Fisher's exact test), Q value = 0.00024
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1067 | 12 |
subtype1 | 318 | 12 |
subtype2 | 131 | 0 |
subtype3 | 295 | 0 |
subtype4 | 294 | 0 |
subtype5 | 29 | 0 |
P value = 0.0588 (Fisher's exact test), Q value = 0.1
nPatients | NO | YES |
---|---|---|
ALL | 437 | 547 |
subtype1 | 135 | 167 |
subtype2 | 42 | 79 |
subtype3 | 134 | 136 |
subtype4 | 111 | 152 |
subtype5 | 15 | 13 |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER, SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 768 | 201 | 6 | 9 | 30 | 17 | 46 |
subtype1 | 0 | 262 | 41 | 0 | 2 | 11 | 4 | 10 |
subtype2 | 0 | 78 | 45 | 0 | 0 | 4 | 1 | 3 |
subtype3 | 0 | 152 | 97 | 0 | 2 | 10 | 11 | 23 |
subtype4 | 1 | 259 | 10 | 5 | 5 | 5 | 0 | 8 |
subtype5 | 0 | 17 | 8 | 1 | 0 | 0 | 1 | 2 |
P value = 0.0269 (Kruskal-Wallis (anova)), Q value = 0.049
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 913 | 2.4 (4.7) |
subtype1 | 258 | 2.4 (3.9) |
subtype2 | 116 | 3.1 (5.6) |
subtype3 | 259 | 2.2 (4.8) |
subtype4 | 256 | 2.1 (4.6) |
subtype5 | 24 | 3.7 (6.0) |
P value = 8e-05 (Fisher's exact test), Q value = 0.00026
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 744 |
subtype1 | 0 | 24 | 49 | 212 |
subtype2 | 0 | 7 | 14 | 101 |
subtype3 | 0 | 11 | 36 | 231 |
subtype4 | 1 | 16 | 75 | 183 |
subtype5 | 0 | 2 | 7 | 17 |
P value = 0.886 (Fisher's exact test), Q value = 0.93
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 39 | 874 |
subtype1 | 10 | 261 |
subtype2 | 4 | 99 |
subtype3 | 13 | 246 |
subtype4 | 12 | 242 |
subtype5 | 0 | 26 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 224 | 184 | 145 | 141 | 88 |
P value = 0.000782 (logrank test), Q value = 0.0021
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 780 | 102 | 0.0 - 282.9 (27.5) |
subtype1 | 223 | 23 | 0.3 - 263.3 (28.3) |
subtype2 | 184 | 35 | 0.0 - 160.9 (24.7) |
subtype3 | 145 | 17 | 1.1 - 216.8 (35.8) |
subtype4 | 140 | 23 | 0.0 - 282.9 (24.7) |
subtype5 | 88 | 4 | 0.2 - 169.5 (25.1) |
P value = 4.65e-05 (Kruskal-Wallis (anova)), Q value = 0.00018
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 769 | 58.2 (13.1) |
subtype1 | 219 | 58.5 (13.4) |
subtype2 | 184 | 61.8 (12.9) |
subtype3 | 143 | 56.5 (12.1) |
subtype4 | 138 | 55.7 (12.5) |
subtype5 | 85 | 56.5 (14.0) |
P value = 0.00251 (Fisher's exact test), Q value = 0.0059
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 60 | 61 | 5 | 6 | 244 | 187 | 2 | 126 | 18 | 53 | 11 | 5 |
subtype1 | 17 | 19 | 3 | 1 | 60 | 63 | 0 | 39 | 5 | 12 | 1 | 3 |
subtype2 | 8 | 11 | 0 | 2 | 53 | 41 | 1 | 38 | 8 | 16 | 4 | 1 |
subtype3 | 22 | 10 | 1 | 1 | 47 | 26 | 1 | 23 | 3 | 9 | 2 | 0 |
subtype4 | 6 | 9 | 1 | 1 | 63 | 38 | 0 | 13 | 1 | 5 | 2 | 1 |
subtype5 | 7 | 12 | 0 | 1 | 21 | 19 | 0 | 13 | 1 | 11 | 2 | 0 |
P value = 0.00041 (Fisher's exact test), Q value = 0.0011
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 199 | 447 | 109 | 24 |
subtype1 | 61 | 129 | 27 | 5 |
subtype2 | 30 | 109 | 34 | 11 |
subtype3 | 54 | 69 | 19 | 3 |
subtype4 | 26 | 96 | 15 | 3 |
subtype5 | 28 | 44 | 14 | 2 |
P value = 0.0156 (Fisher's exact test), Q value = 0.031
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 349 | 269 | 95 | 57 |
subtype1 | 86 | 91 | 29 | 13 |
subtype2 | 74 | 59 | 29 | 17 |
subtype3 | 69 | 48 | 18 | 10 |
subtype4 | 83 | 40 | 11 | 6 |
subtype5 | 37 | 31 | 8 | 11 |
P value = 0.3 (Fisher's exact test), Q value = 0.39
nPatients | 0 | 1 |
---|---|---|
ALL | 609 | 13 |
subtype1 | 180 | 1 |
subtype2 | 136 | 5 |
subtype3 | 114 | 2 |
subtype4 | 112 | 3 |
subtype5 | 67 | 2 |
P value = 0.0439 (Fisher's exact test), Q value = 0.078
nPatients | FEMALE | MALE |
---|---|---|
ALL | 773 | 9 |
subtype1 | 222 | 2 |
subtype2 | 180 | 4 |
subtype3 | 145 | 0 |
subtype4 | 141 | 0 |
subtype5 | 85 | 3 |
P value = 0.97 (Fisher's exact test), Q value = 0.97
nPatients | NO | YES |
---|---|---|
ALL | 316 | 412 |
subtype1 | 93 | 116 |
subtype2 | 74 | 98 |
subtype3 | 56 | 80 |
subtype4 | 58 | 71 |
subtype5 | 35 | 47 |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER, SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 511 | 179 | 6 | 9 | 26 | 15 | 34 |
subtype1 | 0 | 140 | 52 | 0 | 0 | 12 | 5 | 15 |
subtype2 | 0 | 128 | 42 | 0 | 0 | 6 | 4 | 4 |
subtype3 | 0 | 82 | 50 | 2 | 3 | 4 | 1 | 3 |
subtype4 | 1 | 114 | 5 | 4 | 6 | 1 | 0 | 9 |
subtype5 | 0 | 47 | 30 | 0 | 0 | 3 | 5 | 3 |
P value = 0.0147 (Kruskal-Wallis (anova)), Q value = 0.03
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 717 | 2.6 (4.9) |
subtype1 | 211 | 2.4 (4.2) |
subtype2 | 163 | 3.4 (5.8) |
subtype3 | 136 | 2.4 (5.1) |
subtype4 | 130 | 1.7 (3.4) |
subtype5 | 77 | 3.3 (5.7) |
P value = 2e-05 (Fisher's exact test), Q value = 8.7e-05
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 38 | 160 | 568 |
subtype1 | 0 | 10 | 32 | 179 |
subtype2 | 0 | 11 | 35 | 134 |
subtype3 | 1 | 7 | 26 | 108 |
subtype4 | 0 | 7 | 56 | 75 |
subtype5 | 0 | 3 | 11 | 72 |
P value = 0.9 (Fisher's exact test), Q value = 0.94
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 38 | 675 |
subtype1 | 12 | 190 |
subtype2 | 11 | 162 |
subtype3 | 7 | 127 |
subtype4 | 5 | 122 |
subtype5 | 3 | 74 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
---|---|---|---|---|---|---|---|
Number of samples | 199 | 239 | 30 | 208 | 133 | 67 | 10 |
P value = 0.00212 (logrank test), Q value = 0.0051
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 874 | 122 | 0.0 - 282.9 (27.7) |
subtype1 | 194 | 32 | 0.0 - 282.9 (22.0) |
subtype2 | 238 | 32 | 0.2 - 170.2 (27.6) |
subtype3 | 30 | 6 | 0.3 - 89.1 (17.0) |
subtype4 | 205 | 21 | 0.3 - 263.3 (37.7) |
subtype5 | 130 | 19 | 0.3 - 212.2 (26.5) |
subtype6 | 67 | 7 | 0.2 - 106.8 (24.4) |
subtype7 | 10 | 5 | 1.0 - 146.5 (30.2) |
P value = 0.0152 (Kruskal-Wallis (anova)), Q value = 0.03
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 872 | 58.4 (13.3) |
subtype1 | 195 | 57.4 (13.6) |
subtype2 | 235 | 60.9 (13.7) |
subtype3 | 29 | 61.7 (14.9) |
subtype4 | 204 | 57.0 (12.8) |
subtype5 | 133 | 58.4 (12.9) |
subtype6 | 66 | 55.4 (11.7) |
subtype7 | 10 | 55.7 (10.1) |
P value = 2e-05 (Fisher's exact test), Q value = 8.7e-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 X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 62 | 64 | 4 | 4 | 296 | 213 | 2 | 134 | 23 | 53 | 18 | 6 |
subtype1 | 6 | 11 | 0 | 3 | 80 | 52 | 0 | 21 | 3 | 14 | 7 | 0 |
subtype2 | 17 | 22 | 1 | 0 | 73 | 63 | 1 | 38 | 6 | 10 | 4 | 3 |
subtype3 | 3 | 5 | 0 | 0 | 8 | 5 | 0 | 4 | 2 | 0 | 0 | 1 |
subtype4 | 22 | 18 | 1 | 1 | 52 | 58 | 1 | 34 | 4 | 12 | 3 | 1 |
subtype5 | 9 | 2 | 2 | 0 | 55 | 21 | 0 | 23 | 6 | 10 | 3 | 1 |
subtype6 | 5 | 6 | 0 | 0 | 27 | 12 | 0 | 14 | 0 | 3 | 0 | 0 |
subtype7 | 0 | 0 | 0 | 0 | 1 | 2 | 0 | 0 | 2 | 4 | 1 | 0 |
P value = 3e-05 (Fisher's exact test), Q value = 0.00012
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 201 | 533 | 115 | 36 |
subtype1 | 31 | 138 | 24 | 6 |
subtype2 | 57 | 143 | 30 | 8 |
subtype3 | 10 | 14 | 2 | 4 |
subtype4 | 66 | 104 | 33 | 5 |
subtype5 | 21 | 81 | 20 | 11 |
subtype6 | 16 | 45 | 6 | 0 |
subtype7 | 0 | 8 | 0 | 2 |
P value = 0.00962 (Fisher's exact test), Q value = 0.02
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 412 | 291 | 104 | 65 |
subtype1 | 101 | 62 | 19 | 16 |
subtype2 | 107 | 85 | 28 | 13 |
subtype3 | 16 | 5 | 5 | 1 |
subtype4 | 88 | 78 | 25 | 14 |
subtype5 | 63 | 40 | 17 | 12 |
subtype6 | 36 | 18 | 10 | 3 |
subtype7 | 1 | 3 | 0 | 6 |
P value = 0.259 (Fisher's exact test), Q value = 0.34
nPatients | 0 | 1 |
---|---|---|
ALL | 739 | 20 |
subtype1 | 161 | 8 |
subtype2 | 201 | 4 |
subtype3 | 28 | 0 |
subtype4 | 175 | 4 |
subtype5 | 102 | 3 |
subtype6 | 63 | 0 |
subtype7 | 9 | 1 |
P value = 0.18 (Fisher's exact test), Q value = 0.26
nPatients | FEMALE | MALE |
---|---|---|
ALL | 876 | 10 |
subtype1 | 197 | 2 |
subtype2 | 234 | 5 |
subtype3 | 30 | 0 |
subtype4 | 206 | 2 |
subtype5 | 133 | 0 |
subtype6 | 67 | 0 |
subtype7 | 9 | 1 |
P value = 0.00175 (Fisher's exact test), Q value = 0.0043
nPatients | NO | YES |
---|---|---|
ALL | 365 | 448 |
subtype1 | 87 | 92 |
subtype2 | 112 | 110 |
subtype3 | 9 | 17 |
subtype4 | 66 | 129 |
subtype5 | 65 | 58 |
subtype6 | 25 | 36 |
subtype7 | 1 | 6 |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER, SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 642 | 155 | 6 | 7 | 23 | 14 | 38 |
subtype1 | 0 | 167 | 12 | 4 | 2 | 3 | 2 | 9 |
subtype2 | 0 | 166 | 40 | 0 | 0 | 9 | 7 | 17 |
subtype3 | 0 | 24 | 4 | 0 | 1 | 1 | 0 | 0 |
subtype4 | 0 | 130 | 69 | 1 | 0 | 5 | 1 | 2 |
subtype5 | 1 | 92 | 23 | 0 | 3 | 4 | 4 | 6 |
subtype6 | 0 | 56 | 5 | 1 | 1 | 1 | 0 | 3 |
subtype7 | 0 | 7 | 2 | 0 | 0 | 0 | 0 | 1 |
P value = 0.0508 (Kruskal-Wallis (anova)), Q value = 0.088
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 758 | 2.4 (4.7) |
subtype1 | 166 | 2.6 (5.3) |
subtype2 | 203 | 2.2 (4.1) |
subtype3 | 19 | 1.5 (3.4) |
subtype4 | 195 | 2.6 (5.1) |
subtype5 | 108 | 2.0 (3.7) |
subtype6 | 60 | 2.1 (3.6) |
subtype7 | 7 | 11.0 (11.2) |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 59 | 137 | 629 |
subtype1 | 0 | 19 | 57 | 112 |
subtype2 | 0 | 12 | 26 | 184 |
subtype3 | 0 | 1 | 4 | 19 |
subtype4 | 0 | 12 | 18 | 168 |
subtype5 | 0 | 10 | 23 | 89 |
subtype6 | 1 | 5 | 8 | 51 |
subtype7 | 0 | 0 | 1 | 6 |
P value = 0.654 (Fisher's exact test), Q value = 0.75
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 28 | 730 |
subtype1 | 6 | 170 |
subtype2 | 8 | 196 |
subtype3 | 1 | 22 |
subtype4 | 10 | 164 |
subtype5 | 2 | 110 |
subtype6 | 1 | 61 |
subtype7 | 0 | 7 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 225 | 401 | 260 |
P value = 0.101 (logrank test), Q value = 0.16
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 874 | 122 | 0.0 - 282.9 (27.7) |
subtype1 | 222 | 37 | 0.0 - 282.9 (28.3) |
subtype2 | 396 | 54 | 0.2 - 170.2 (24.6) |
subtype3 | 256 | 31 | 0.2 - 263.3 (34.3) |
P value = 0.00203 (Kruskal-Wallis (anova)), Q value = 0.005
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 872 | 58.4 (13.3) |
subtype1 | 222 | 56.0 (13.1) |
subtype2 | 393 | 59.8 (14.1) |
subtype3 | 257 | 58.3 (12.0) |
P value = 0.0982 (Fisher's exact test), Q value = 0.16
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 62 | 64 | 4 | 4 | 296 | 213 | 2 | 134 | 23 | 53 | 18 | 6 |
subtype1 | 9 | 13 | 0 | 1 | 98 | 50 | 1 | 26 | 4 | 15 | 4 | 0 |
subtype2 | 29 | 33 | 1 | 2 | 118 | 97 | 1 | 66 | 14 | 24 | 10 | 5 |
subtype3 | 24 | 18 | 3 | 1 | 80 | 66 | 0 | 42 | 5 | 14 | 4 | 1 |
P value = 0.205 (Fisher's exact test), Q value = 0.28
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 201 | 533 | 115 | 36 |
subtype1 | 41 | 150 | 25 | 9 |
subtype2 | 89 | 240 | 53 | 18 |
subtype3 | 71 | 143 | 37 | 9 |
P value = 0.536 (Fisher's exact test), Q value = 0.64
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 412 | 291 | 104 | 65 |
subtype1 | 114 | 70 | 20 | 18 |
subtype2 | 184 | 126 | 52 | 29 |
subtype3 | 114 | 95 | 32 | 18 |
P value = 0.957 (Fisher's exact test), Q value = 0.97
nPatients | 0 | 1 |
---|---|---|
ALL | 739 | 20 |
subtype1 | 197 | 5 |
subtype2 | 330 | 10 |
subtype3 | 212 | 5 |
P value = 0.0718 (Fisher's exact test), Q value = 0.12
nPatients | FEMALE | MALE |
---|---|---|
ALL | 876 | 10 |
subtype1 | 225 | 0 |
subtype2 | 393 | 8 |
subtype3 | 258 | 2 |
P value = 0.177 (Fisher's exact test), Q value = 0.26
nPatients | NO | YES |
---|---|---|
ALL | 365 | 448 |
subtype1 | 92 | 109 |
subtype2 | 177 | 195 |
subtype3 | 96 | 144 |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER, SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 642 | 155 | 6 | 7 | 23 | 14 | 38 |
subtype1 | 1 | 199 | 7 | 3 | 4 | 0 | 0 | 11 |
subtype2 | 0 | 285 | 60 | 2 | 1 | 17 | 13 | 23 |
subtype3 | 0 | 158 | 88 | 1 | 2 | 6 | 1 | 4 |
P value = 0.486 (Kruskal-Wallis (anova)), Q value = 0.59
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 758 | 2.4 (4.7) |
subtype1 | 191 | 2.5 (5.3) |
subtype2 | 330 | 2.5 (4.6) |
subtype3 | 237 | 2.3 (4.4) |
P value = 0.00013 (Fisher's exact test), Q value = 0.00039
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 59 | 137 | 629 |
subtype1 | 1 | 21 | 49 | 140 |
subtype2 | 0 | 26 | 65 | 283 |
subtype3 | 0 | 12 | 23 | 206 |
P value = 0.373 (Fisher's exact test), Q value = 0.47
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 28 | 730 |
subtype1 | 5 | 192 |
subtype2 | 12 | 336 |
subtype3 | 11 | 202 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
---|---|---|---|---|---|---|---|
Number of samples | 267 | 171 | 147 | 227 | 209 | 52 | 20 |
P value = 4.93e-05 (logrank test), Q value = 0.00018
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 1079 | 151 | 0.0 - 282.9 (28.3) |
subtype1 | 262 | 35 | 0.2 - 188.7 (29.2) |
subtype2 | 167 | 39 | 0.0 - 212.2 (24.3) |
subtype3 | 147 | 13 | 0.3 - 169.5 (36.2) |
subtype4 | 225 | 24 | 0.3 - 281.3 (25.7) |
subtype5 | 207 | 29 | 0.0 - 282.9 (27.0) |
subtype6 | 51 | 6 | 2.1 - 216.8 (27.9) |
subtype7 | 20 | 5 | 12.3 - 130.2 (47.2) |
P value = 7.1e-07 (Kruskal-Wallis (anova)), Q value = 5e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1078 | 58.6 (13.2) |
subtype1 | 262 | 59.3 (14.5) |
subtype2 | 165 | 59.9 (13.2) |
subtype3 | 145 | 54.9 (11.7) |
subtype4 | 225 | 61.3 (12.6) |
subtype5 | 209 | 55.6 (12.3) |
subtype6 | 52 | 61.1 (11.7) |
subtype7 | 20 | 59.8 (13.6) |
P value = 0.00279 (Fisher's exact test), Q value = 0.0065
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 90 | 85 | 6 | 6 | 358 | 256 | 2 | 156 | 27 | 65 | 20 | 14 |
subtype1 | 18 | 16 | 4 | 1 | 81 | 73 | 1 | 44 | 12 | 10 | 3 | 4 |
subtype2 | 10 | 12 | 0 | 1 | 54 | 38 | 0 | 28 | 6 | 12 | 6 | 2 |
subtype3 | 12 | 14 | 1 | 1 | 31 | 40 | 1 | 25 | 0 | 16 | 3 | 2 |
subtype4 | 25 | 24 | 1 | 1 | 77 | 43 | 0 | 29 | 5 | 10 | 4 | 5 |
subtype5 | 14 | 15 | 0 | 1 | 93 | 47 | 0 | 22 | 4 | 7 | 3 | 1 |
subtype6 | 5 | 3 | 0 | 1 | 16 | 11 | 0 | 6 | 0 | 9 | 1 | 0 |
subtype7 | 6 | 1 | 0 | 0 | 6 | 4 | 0 | 2 | 0 | 1 | 0 | 0 |
P value = 1e-04 (Fisher's exact test), Q value = 0.00032
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 279 | 633 | 138 | 40 |
subtype1 | 61 | 164 | 27 | 13 |
subtype2 | 38 | 106 | 17 | 10 |
subtype3 | 44 | 72 | 31 | 0 |
subtype4 | 78 | 114 | 26 | 9 |
subtype5 | 41 | 137 | 23 | 7 |
subtype6 | 10 | 28 | 13 | 1 |
subtype7 | 7 | 12 | 1 | 0 |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 515 | 361 | 120 | 77 |
subtype1 | 106 | 105 | 36 | 11 |
subtype2 | 65 | 58 | 27 | 16 |
subtype3 | 56 | 56 | 14 | 18 |
subtype4 | 118 | 72 | 20 | 14 |
subtype5 | 129 | 54 | 18 | 8 |
subtype6 | 28 | 12 | 3 | 9 |
subtype7 | 13 | 4 | 2 | 1 |
P value = 0.848 (Fisher's exact test), Q value = 0.9
nPatients | 0 | 1 |
---|---|---|
ALL | 903 | 22 |
subtype1 | 225 | 4 |
subtype2 | 144 | 6 |
subtype3 | 119 | 3 |
subtype4 | 186 | 4 |
subtype5 | 178 | 4 |
subtype6 | 35 | 1 |
subtype7 | 16 | 0 |
P value = 0.0218 (Fisher's exact test), Q value = 0.041
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1081 | 12 |
subtype1 | 258 | 9 |
subtype2 | 170 | 1 |
subtype3 | 147 | 0 |
subtype4 | 225 | 2 |
subtype5 | 209 | 0 |
subtype6 | 52 | 0 |
subtype7 | 20 | 0 |
P value = 0.818 (Fisher's exact test), Q value = 0.88
nPatients | NO | YES |
---|---|---|
ALL | 445 | 553 |
subtype1 | 112 | 134 |
subtype2 | 72 | 74 |
subtype3 | 59 | 80 |
subtype4 | 95 | 116 |
subtype5 | 81 | 107 |
subtype6 | 19 | 30 |
subtype7 | 7 | 12 |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER, SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 782 | 203 | 6 | 9 | 29 | 17 | 45 |
subtype1 | 0 | 215 | 26 | 0 | 0 | 6 | 9 | 11 |
subtype2 | 0 | 152 | 12 | 0 | 1 | 2 | 0 | 4 |
subtype3 | 0 | 67 | 65 | 0 | 0 | 9 | 1 | 5 |
subtype4 | 0 | 136 | 64 | 0 | 0 | 9 | 4 | 14 |
subtype5 | 1 | 177 | 2 | 5 | 8 | 2 | 3 | 10 |
subtype6 | 0 | 18 | 32 | 0 | 0 | 1 | 0 | 1 |
subtype7 | 0 | 17 | 2 | 1 | 0 | 0 | 0 | 0 |
P value = 1.62e-05 (Kruskal-Wallis (anova)), Q value = 7.5e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 925 | 2.4 (4.6) |
subtype1 | 217 | 2.2 (3.8) |
subtype2 | 123 | 3.3 (5.8) |
subtype3 | 135 | 3.4 (6.1) |
subtype4 | 190 | 2.0 (4.0) |
subtype5 | 191 | 1.3 (2.9) |
subtype6 | 50 | 3.5 (6.2) |
subtype7 | 19 | 2.1 (5.3) |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 61 | 183 | 753 |
subtype1 | 0 | 16 | 47 | 177 |
subtype2 | 1 | 21 | 24 | 99 |
subtype3 | 0 | 6 | 13 | 123 |
subtype4 | 0 | 9 | 23 | 172 |
subtype5 | 0 | 8 | 69 | 122 |
subtype6 | 0 | 0 | 2 | 46 |
subtype7 | 0 | 1 | 5 | 14 |
P value = 0.366 (Fisher's exact test), Q value = 0.47
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 39 | 880 |
subtype1 | 9 | 211 |
subtype2 | 2 | 133 |
subtype3 | 7 | 120 |
subtype4 | 12 | 176 |
subtype5 | 6 | 178 |
subtype6 | 2 | 43 |
subtype7 | 1 | 19 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 294 | 166 | 91 | 294 | 188 | 60 |
P value = 3.31e-06 (logrank test), Q value = 5e-05
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 1079 | 151 | 0.0 - 282.9 (28.3) |
subtype1 | 288 | 41 | 0.2 - 275.9 (25.5) |
subtype2 | 163 | 36 | 0.0 - 212.2 (23.1) |
subtype3 | 91 | 9 | 0.3 - 169.5 (38.2) |
subtype4 | 293 | 26 | 0.3 - 281.3 (32.5) |
subtype5 | 186 | 27 | 0.2 - 282.9 (28.4) |
subtype6 | 58 | 12 | 0.0 - 102.8 (20.2) |
P value = 1.37e-10 (Kruskal-Wallis (anova)), Q value = 2e-08
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1078 | 58.6 (13.2) |
subtype1 | 287 | 61.9 (13.9) |
subtype2 | 162 | 61.8 (12.8) |
subtype3 | 90 | 56.3 (12.4) |
subtype4 | 293 | 56.4 (12.5) |
subtype5 | 188 | 55.0 (12.1) |
subtype6 | 58 | 59.4 (13.1) |
P value = 1e-05 (Fisher's exact test), Q value = 5e-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 X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 90 | 85 | 6 | 6 | 358 | 256 | 2 | 156 | 27 | 65 | 20 | 14 |
subtype1 | 20 | 23 | 4 | 2 | 94 | 75 | 1 | 43 | 13 | 7 | 4 | 6 |
subtype2 | 7 | 8 | 0 | 1 | 51 | 38 | 0 | 31 | 8 | 12 | 7 | 2 |
subtype3 | 7 | 9 | 1 | 1 | 17 | 27 | 0 | 14 | 1 | 12 | 1 | 0 |
subtype4 | 42 | 25 | 1 | 1 | 87 | 62 | 0 | 44 | 0 | 23 | 3 | 5 |
subtype5 | 13 | 15 | 0 | 1 | 86 | 41 | 0 | 17 | 4 | 5 | 3 | 1 |
subtype6 | 1 | 5 | 0 | 0 | 23 | 13 | 1 | 7 | 1 | 6 | 2 | 0 |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 279 | 633 | 138 | 40 |
subtype1 | 76 | 170 | 28 | 18 |
subtype2 | 25 | 110 | 21 | 10 |
subtype3 | 25 | 38 | 27 | 1 |
subtype4 | 95 | 156 | 41 | 2 |
subtype5 | 40 | 124 | 17 | 6 |
subtype6 | 18 | 35 | 4 | 3 |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 515 | 361 | 120 | 77 |
subtype1 | 126 | 115 | 33 | 12 |
subtype2 | 66 | 48 | 31 | 14 |
subtype3 | 38 | 36 | 5 | 12 |
subtype4 | 147 | 89 | 29 | 25 |
subtype5 | 117 | 51 | 14 | 6 |
subtype6 | 21 | 22 | 8 | 8 |
P value = 0.28 (Fisher's exact test), Q value = 0.37
nPatients | 0 | 1 |
---|---|---|
ALL | 903 | 22 |
subtype1 | 250 | 5 |
subtype2 | 134 | 7 |
subtype3 | 70 | 1 |
subtype4 | 235 | 3 |
subtype5 | 162 | 4 |
subtype6 | 52 | 2 |
P value = 0.0189 (Fisher's exact test), Q value = 0.036
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1081 | 12 |
subtype1 | 285 | 9 |
subtype2 | 164 | 2 |
subtype3 | 91 | 0 |
subtype4 | 293 | 1 |
subtype5 | 188 | 0 |
subtype6 | 60 | 0 |
P value = 0.177 (Fisher's exact test), Q value = 0.26
nPatients | NO | YES |
---|---|---|
ALL | 445 | 553 |
subtype1 | 129 | 143 |
subtype2 | 70 | 74 |
subtype3 | 42 | 44 |
subtype4 | 106 | 168 |
subtype5 | 72 | 99 |
subtype6 | 26 | 25 |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER, SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 782 | 203 | 6 | 9 | 29 | 17 | 45 |
subtype1 | 0 | 224 | 24 | 0 | 0 | 10 | 15 | 21 |
subtype2 | 0 | 138 | 16 | 0 | 3 | 4 | 1 | 4 |
subtype3 | 0 | 27 | 56 | 0 | 0 | 5 | 1 | 2 |
subtype4 | 0 | 176 | 100 | 1 | 0 | 8 | 0 | 9 |
subtype5 | 1 | 163 | 2 | 5 | 5 | 2 | 0 | 9 |
subtype6 | 0 | 54 | 5 | 0 | 1 | 0 | 0 | 0 |
P value = 3.56e-05 (Kruskal-Wallis (anova)), Q value = 0.00014
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 925 | 2.4 (4.6) |
subtype1 | 233 | 1.9 (3.3) |
subtype2 | 121 | 3.1 (5.0) |
subtype3 | 87 | 3.7 (6.5) |
subtype4 | 268 | 2.4 (4.8) |
subtype5 | 173 | 1.3 (2.9) |
subtype6 | 43 | 4.2 (7.8) |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 61 | 183 | 753 |
subtype1 | 0 | 19 | 42 | 197 |
subtype2 | 0 | 14 | 20 | 106 |
subtype3 | 0 | 3 | 9 | 77 |
subtype4 | 0 | 8 | 34 | 235 |
subtype5 | 0 | 5 | 65 | 110 |
subtype6 | 1 | 12 | 13 | 28 |
P value = 0.548 (Fisher's exact test), Q value = 0.65
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 39 | 880 |
subtype1 | 12 | 229 |
subtype2 | 3 | 129 |
subtype3 | 2 | 77 |
subtype4 | 15 | 236 |
subtype5 | 6 | 159 |
subtype6 | 1 | 50 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 140 | 274 | 211 | 218 | 187 | 47 |
P value = 0.607 (logrank test), Q value = 0.71
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 1063 | 147 | 0.0 - 282.9 (28.1) |
subtype1 | 138 | 20 | 0.0 - 275.9 (29.9) |
subtype2 | 269 | 40 | 0.2 - 255.7 (24.3) |
subtype3 | 206 | 22 | 0.2 - 263.3 (25.1) |
subtype4 | 218 | 28 | 0.0 - 282.9 (32.8) |
subtype5 | 185 | 30 | 0.3 - 234.3 (26.1) |
subtype6 | 47 | 7 | 1.7 - 281.3 (34.4) |
P value = 0.00513 (Kruskal-Wallis (anova)), Q value = 0.011
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1062 | 58.6 (13.2) |
subtype1 | 134 | 57.1 (14.1) |
subtype2 | 273 | 57.8 (13.0) |
subtype3 | 210 | 61.0 (13.6) |
subtype4 | 214 | 57.4 (12.7) |
subtype5 | 185 | 59.8 (13.0) |
subtype6 | 46 | 58.2 (11.7) |
P value = 0.00945 (Fisher's exact test), Q value = 0.02
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 89 | 85 | 7 | 6 | 353 | 250 | 2 | 153 | 26 | 64 | 20 | 14 |
subtype1 | 14 | 6 | 0 | 1 | 44 | 35 | 1 | 24 | 2 | 9 | 2 | 2 |
subtype2 | 10 | 17 | 1 | 1 | 117 | 57 | 0 | 37 | 7 | 12 | 8 | 3 |
subtype3 | 13 | 22 | 3 | 1 | 66 | 47 | 0 | 31 | 8 | 15 | 1 | 4 |
subtype4 | 23 | 19 | 1 | 2 | 53 | 59 | 1 | 33 | 3 | 20 | 3 | 0 |
subtype5 | 23 | 17 | 1 | 1 | 59 | 38 | 0 | 25 | 5 | 7 | 5 | 4 |
subtype6 | 6 | 4 | 1 | 0 | 14 | 14 | 0 | 3 | 1 | 1 | 1 | 1 |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 279 | 620 | 135 | 40 |
subtype1 | 31 | 85 | 19 | 4 |
subtype2 | 45 | 191 | 26 | 11 |
subtype3 | 55 | 118 | 28 | 9 |
subtype4 | 70 | 102 | 43 | 3 |
subtype5 | 66 | 99 | 12 | 10 |
subtype6 | 12 | 25 | 7 | 3 |
P value = 0.256 (Fisher's exact test), Q value = 0.34
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 508 | 356 | 118 | 75 |
subtype1 | 58 | 49 | 18 | 10 |
subtype2 | 146 | 74 | 34 | 15 |
subtype3 | 99 | 68 | 24 | 15 |
subtype4 | 93 | 85 | 18 | 21 |
subtype5 | 86 | 66 | 21 | 10 |
subtype6 | 26 | 14 | 3 | 4 |
P value = 0.694 (Fisher's exact test), Q value = 0.78
nPatients | 0 | 1 |
---|---|---|
ALL | 887 | 21 |
subtype1 | 120 | 2 |
subtype2 | 230 | 8 |
subtype3 | 170 | 2 |
subtype4 | 165 | 3 |
subtype5 | 164 | 5 |
subtype6 | 38 | 1 |
P value = 0.336 (Fisher's exact test), Q value = 0.43
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1065 | 12 |
subtype1 | 139 | 1 |
subtype2 | 270 | 4 |
subtype3 | 208 | 3 |
subtype4 | 218 | 0 |
subtype5 | 183 | 4 |
subtype6 | 47 | 0 |
P value = 0.914 (Fisher's exact test), Q value = 0.94
nPatients | NO | YES |
---|---|---|
ALL | 441 | 543 |
subtype1 | 61 | 70 |
subtype2 | 111 | 135 |
subtype3 | 84 | 111 |
subtype4 | 86 | 117 |
subtype5 | 79 | 87 |
subtype6 | 20 | 23 |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER, SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 768 | 200 | 6 | 9 | 29 | 17 | 46 |
subtype1 | 0 | 106 | 17 | 1 | 0 | 5 | 4 | 7 |
subtype2 | 1 | 245 | 4 | 5 | 5 | 3 | 1 | 9 |
subtype3 | 0 | 135 | 48 | 0 | 0 | 7 | 9 | 12 |
subtype4 | 0 | 95 | 106 | 0 | 4 | 5 | 3 | 5 |
subtype5 | 0 | 154 | 14 | 0 | 0 | 8 | 0 | 11 |
subtype6 | 0 | 33 | 11 | 0 | 0 | 1 | 0 | 2 |
P value = 0.105 (Kruskal-Wallis (anova)), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 915 | 2.4 (4.6) |
subtype1 | 117 | 2.7 (5.3) |
subtype2 | 227 | 2.0 (4.4) |
subtype3 | 171 | 2.5 (4.6) |
subtype4 | 206 | 2.9 (5.4) |
subtype5 | 158 | 1.8 (3.2) |
subtype6 | 36 | 2.2 (4.7) |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 61 | 182 | 745 |
subtype1 | 0 | 17 | 21 | 97 |
subtype2 | 0 | 11 | 81 | 156 |
subtype3 | 0 | 8 | 37 | 141 |
subtype4 | 1 | 13 | 29 | 171 |
subtype5 | 0 | 11 | 7 | 148 |
subtype6 | 0 | 1 | 7 | 32 |
P value = 0.372 (Fisher's exact test), Q value = 0.47
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 39 | 873 |
subtype1 | 9 | 122 |
subtype2 | 6 | 222 |
subtype3 | 8 | 161 |
subtype4 | 9 | 193 |
subtype5 | 7 | 137 |
subtype6 | 0 | 38 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |
---|---|---|---|---|---|---|---|---|---|
Number of samples | 68 | 124 | 187 | 188 | 73 | 117 | 163 | 73 | 84 |
P value = 0.0316 (logrank test), Q value = 0.057
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 1063 | 147 | 0.0 - 282.9 (28.1) |
subtype1 | 65 | 12 | 2.4 - 165.8 (32.9) |
subtype2 | 120 | 23 | 0.0 - 146.5 (25.9) |
subtype3 | 187 | 20 | 0.3 - 140.3 (33.4) |
subtype4 | 184 | 22 | 0.2 - 275.9 (29.5) |
subtype5 | 72 | 6 | 0.3 - 281.3 (35.6) |
subtype6 | 117 | 20 | 0.3 - 263.3 (28.8) |
subtype7 | 161 | 27 | 0.2 - 282.9 (30.2) |
subtype8 | 73 | 4 | 1.1 - 170.2 (21.1) |
subtype9 | 84 | 13 | 0.3 - 216.8 (19.5) |
P value = 6.34e-05 (Kruskal-Wallis (anova)), Q value = 0.00022
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1062 | 58.6 (13.2) |
subtype1 | 66 | 59.6 (13.3) |
subtype2 | 119 | 59.4 (12.8) |
subtype3 | 185 | 58.3 (12.1) |
subtype4 | 187 | 58.9 (15.4) |
subtype5 | 73 | 57.8 (11.6) |
subtype6 | 116 | 60.0 (12.5) |
subtype7 | 163 | 54.3 (11.9) |
subtype8 | 70 | 62.6 (14.2) |
subtype9 | 83 | 60.9 (12.8) |
P value = 3e-05 (Fisher's exact test), Q value = 0.00012
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 89 | 85 | 7 | 6 | 353 | 250 | 2 | 153 | 26 | 64 | 20 | 14 |
subtype1 | 2 | 5 | 0 | 1 | 17 | 20 | 0 | 13 | 4 | 3 | 1 | 2 |
subtype2 | 13 | 6 | 1 | 1 | 43 | 30 | 0 | 13 | 3 | 9 | 2 | 1 |
subtype3 | 17 | 18 | 1 | 1 | 38 | 50 | 1 | 35 | 1 | 22 | 1 | 1 |
subtype4 | 17 | 18 | 2 | 0 | 60 | 46 | 0 | 32 | 7 | 1 | 1 | 3 |
subtype5 | 12 | 3 | 1 | 0 | 22 | 17 | 0 | 5 | 2 | 6 | 3 | 1 |
subtype6 | 8 | 10 | 1 | 1 | 48 | 17 | 0 | 17 | 3 | 3 | 4 | 4 |
subtype7 | 11 | 15 | 0 | 1 | 74 | 31 | 0 | 14 | 4 | 6 | 3 | 2 |
subtype8 | 4 | 6 | 1 | 0 | 22 | 19 | 1 | 9 | 2 | 8 | 1 | 0 |
subtype9 | 5 | 4 | 0 | 1 | 29 | 20 | 0 | 15 | 0 | 6 | 4 | 0 |
P value = 5e-05 (Fisher's exact test), Q value = 0.00018
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 279 | 620 | 135 | 40 |
subtype1 | 11 | 42 | 10 | 4 |
subtype2 | 33 | 74 | 11 | 6 |
subtype3 | 53 | 85 | 47 | 2 |
subtype4 | 59 | 97 | 23 | 8 |
subtype5 | 18 | 44 | 5 | 6 |
subtype6 | 33 | 71 | 8 | 5 |
subtype7 | 39 | 105 | 12 | 6 |
subtype8 | 17 | 44 | 9 | 3 |
subtype9 | 16 | 58 | 10 | 0 |
P value = 8e-05 (Fisher's exact test), Q value = 0.00026
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 508 | 356 | 118 | 75 |
subtype1 | 26 | 26 | 11 | 3 |
subtype2 | 57 | 39 | 14 | 11 |
subtype3 | 78 | 65 | 20 | 24 |
subtype4 | 87 | 74 | 21 | 1 |
subtype5 | 40 | 20 | 5 | 8 |
subtype6 | 54 | 41 | 12 | 6 |
subtype7 | 100 | 43 | 12 | 7 |
subtype8 | 29 | 25 | 8 | 9 |
subtype9 | 37 | 23 | 15 | 6 |
P value = 0.112 (Fisher's exact test), Q value = 0.18
nPatients | 0 | 1 |
---|---|---|
ALL | 887 | 21 |
subtype1 | 62 | 1 |
subtype2 | 112 | 2 |
subtype3 | 135 | 1 |
subtype4 | 160 | 1 |
subtype5 | 62 | 3 |
subtype6 | 99 | 5 |
subtype7 | 139 | 3 |
subtype8 | 54 | 1 |
subtype9 | 64 | 4 |
P value = 0.134 (Fisher's exact test), Q value = 0.21
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1065 | 12 |
subtype1 | 66 | 2 |
subtype2 | 122 | 2 |
subtype3 | 187 | 0 |
subtype4 | 184 | 4 |
subtype5 | 72 | 1 |
subtype6 | 115 | 2 |
subtype7 | 163 | 0 |
subtype8 | 73 | 0 |
subtype9 | 83 | 1 |
P value = 0.738 (Fisher's exact test), Q value = 0.81
nPatients | NO | YES |
---|---|---|
ALL | 441 | 543 |
subtype1 | 34 | 27 |
subtype2 | 47 | 63 |
subtype3 | 74 | 105 |
subtype4 | 78 | 90 |
subtype5 | 31 | 31 |
subtype6 | 47 | 64 |
subtype7 | 64 | 81 |
subtype8 | 32 | 41 |
subtype9 | 34 | 41 |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER, SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 768 | 200 | 6 | 9 | 29 | 17 | 46 |
subtype1 | 0 | 51 | 4 | 0 | 0 | 4 | 5 | 4 |
subtype2 | 0 | 107 | 7 | 1 | 3 | 1 | 0 | 5 |
subtype3 | 0 | 68 | 110 | 0 | 1 | 4 | 1 | 3 |
subtype4 | 0 | 138 | 20 | 0 | 0 | 6 | 8 | 16 |
subtype5 | 0 | 56 | 13 | 0 | 0 | 3 | 0 | 1 |
subtype6 | 0 | 92 | 12 | 0 | 0 | 7 | 0 | 6 |
subtype7 | 1 | 143 | 2 | 5 | 2 | 2 | 0 | 7 |
subtype8 | 0 | 42 | 24 | 0 | 0 | 2 | 3 | 2 |
subtype9 | 0 | 71 | 8 | 0 | 3 | 0 | 0 | 2 |
P value = 0.00337 (Kruskal-Wallis (anova)), Q value = 0.0076
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 915 | 2.4 (4.6) |
subtype1 | 58 | 2.4 (3.8) |
subtype2 | 96 | 2.5 (5.1) |
subtype3 | 170 | 3.5 (6.1) |
subtype4 | 156 | 1.4 (2.2) |
subtype5 | 66 | 2.5 (5.1) |
subtype6 | 90 | 1.8 (3.2) |
subtype7 | 147 | 1.4 (3.0) |
subtype8 | 63 | 3.2 (5.8) |
subtype9 | 69 | 3.3 (6.4) |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 61 | 182 | 745 |
subtype1 | 0 | 6 | 5 | 56 |
subtype2 | 1 | 13 | 12 | 80 |
subtype3 | 0 | 8 | 25 | 151 |
subtype4 | 0 | 7 | 22 | 133 |
subtype5 | 0 | 4 | 8 | 57 |
subtype6 | 0 | 5 | 12 | 82 |
subtype7 | 0 | 7 | 60 | 89 |
subtype8 | 0 | 7 | 24 | 41 |
subtype9 | 0 | 4 | 14 | 56 |
P value = 0.18 (Fisher's exact test), Q value = 0.26
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 39 | 873 |
subtype1 | 0 | 64 |
subtype2 | 4 | 87 |
subtype3 | 4 | 165 |
subtype4 | 12 | 136 |
subtype5 | 4 | 59 |
subtype6 | 4 | 86 |
subtype7 | 5 | 138 |
subtype8 | 4 | 68 |
subtype9 | 2 | 70 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 135 | 94 | 59 | 121 | 145 | 114 |
P value = 0.967 (logrank test), Q value = 0.97
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 664 | 86 | 0.0 - 216.8 (26.7) |
subtype1 | 134 | 17 | 1.1 - 160.9 (21.5) |
subtype2 | 94 | 8 | 0.2 - 110.6 (24.3) |
subtype3 | 59 | 9 | 5.3 - 212.2 (31.4) |
subtype4 | 121 | 19 | 2.8 - 139.2 (35.9) |
subtype5 | 142 | 17 | 0.0 - 130.2 (24.5) |
subtype6 | 114 | 16 | 1.6 - 216.8 (30.1) |
P value = 0.0786 (Kruskal-Wallis (anova)), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 653 | 58.3 (13.2) |
subtype1 | 131 | 60.0 (14.5) |
subtype2 | 92 | 60.5 (12.4) |
subtype3 | 58 | 57.9 (11.5) |
subtype4 | 118 | 56.4 (13.3) |
subtype5 | 143 | 56.6 (12.7) |
subtype6 | 111 | 58.9 (13.3) |
P value = 0.00027 (Fisher's exact test), Q value = 0.00076
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 62 | 51 | 5 | 5 | 219 | 162 | 2 | 92 | 13 | 42 | 8 | 2 |
subtype1 | 10 | 12 | 0 | 1 | 49 | 32 | 1 | 19 | 2 | 8 | 0 | 1 |
subtype2 | 4 | 11 | 3 | 1 | 23 | 22 | 0 | 13 | 1 | 12 | 4 | 0 |
subtype3 | 7 | 6 | 1 | 0 | 12 | 20 | 0 | 9 | 1 | 1 | 1 | 0 |
subtype4 | 18 | 11 | 1 | 1 | 46 | 21 | 0 | 13 | 3 | 3 | 1 | 1 |
subtype5 | 11 | 6 | 0 | 1 | 63 | 33 | 0 | 22 | 3 | 3 | 1 | 0 |
subtype6 | 12 | 5 | 0 | 1 | 26 | 34 | 1 | 16 | 3 | 15 | 1 | 0 |
P value = 4e-05 (Fisher's exact test), Q value = 0.00016
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 184 | 379 | 85 | 19 |
subtype1 | 32 | 79 | 20 | 3 |
subtype2 | 23 | 50 | 18 | 3 |
subtype3 | 21 | 28 | 9 | 1 |
subtype4 | 54 | 57 | 6 | 4 |
subtype5 | 25 | 104 | 11 | 5 |
subtype6 | 29 | 61 | 21 | 3 |
P value = 0.00066 (Fisher's exact test), Q value = 0.0018
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 318 | 229 | 67 | 45 |
subtype1 | 65 | 43 | 14 | 8 |
subtype2 | 41 | 31 | 7 | 13 |
subtype3 | 27 | 25 | 6 | 1 |
subtype4 | 61 | 45 | 10 | 4 |
subtype5 | 82 | 39 | 21 | 3 |
subtype6 | 42 | 46 | 9 | 16 |
P value = 0.021 (Fisher's exact test), Q value = 0.04
nPatients | 0 | 1 |
---|---|---|
ALL | 516 | 8 |
subtype1 | 114 | 0 |
subtype2 | 52 | 4 |
subtype3 | 45 | 1 |
subtype4 | 101 | 1 |
subtype5 | 115 | 1 |
subtype6 | 89 | 1 |
P value = 0.637 (Fisher's exact test), Q value = 0.74
nPatients | FEMALE | MALE |
---|---|---|
ALL | 659 | 9 |
subtype1 | 132 | 3 |
subtype2 | 92 | 2 |
subtype3 | 59 | 0 |
subtype4 | 119 | 2 |
subtype5 | 143 | 2 |
subtype6 | 114 | 0 |
P value = 0.138 (Fisher's exact test), Q value = 0.21
nPatients | NO | YES |
---|---|---|
ALL | 282 | 337 |
subtype1 | 70 | 54 |
subtype2 | 40 | 50 |
subtype3 | 19 | 33 |
subtype4 | 47 | 63 |
subtype5 | 57 | 74 |
subtype6 | 49 | 63 |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER, SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 436 | 161 | 5 | 9 | 16 | 15 | 25 |
subtype1 | 0 | 96 | 17 | 0 | 0 | 5 | 9 | 8 |
subtype2 | 0 | 34 | 55 | 0 | 2 | 1 | 1 | 1 |
subtype3 | 0 | 36 | 14 | 0 | 3 | 1 | 0 | 5 |
subtype4 | 0 | 94 | 15 | 0 | 0 | 6 | 1 | 5 |
subtype5 | 1 | 128 | 2 | 5 | 4 | 2 | 0 | 3 |
subtype6 | 0 | 48 | 58 | 0 | 0 | 1 | 4 | 3 |
P value = 0.0528 (Kruskal-Wallis (anova)), Q value = 0.091
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 600 | 2.5 (5.0) |
subtype1 | 111 | 2.4 (4.8) |
subtype2 | 81 | 3.2 (5.7) |
subtype3 | 56 | 2.1 (4.4) |
subtype4 | 112 | 1.8 (4.0) |
subtype5 | 132 | 1.5 (2.7) |
subtype6 | 108 | 4.0 (7.4) |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 51 | 145 | 466 |
subtype1 | 15 | 25 | 95 |
subtype2 | 1 | 36 | 55 |
subtype3 | 2 | 8 | 48 |
subtype4 | 8 | 3 | 110 |
subtype5 | 15 | 56 | 72 |
subtype6 | 10 | 17 | 86 |
P value = 0.675 (Fisher's exact test), Q value = 0.77
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 29 | 608 |
subtype1 | 6 | 125 |
subtype2 | 4 | 83 |
subtype3 | 3 | 53 |
subtype4 | 7 | 107 |
subtype5 | 3 | 135 |
subtype6 | 6 | 105 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 318 | 233 | 117 |
P value = 0.201 (logrank test), Q value = 0.28
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 664 | 86 | 0.0 - 216.8 (26.7) |
subtype1 | 314 | 49 | 0.2 - 160.9 (27.9) |
subtype2 | 233 | 21 | 0.0 - 216.8 (22.4) |
subtype3 | 117 | 16 | 2.8 - 212.2 (34.5) |
P value = 0.0465 (Kruskal-Wallis (anova)), Q value = 0.082
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 653 | 58.3 (13.2) |
subtype1 | 309 | 57.9 (13.7) |
subtype2 | 228 | 59.8 (12.8) |
subtype3 | 116 | 56.2 (12.4) |
P value = 0.00011 (Fisher's exact test), Q value = 0.00034
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 62 | 51 | 5 | 5 | 219 | 162 | 2 | 92 | 13 | 42 | 8 | 2 |
subtype1 | 25 | 22 | 2 | 3 | 126 | 74 | 0 | 45 | 7 | 8 | 3 | 1 |
subtype2 | 17 | 18 | 3 | 2 | 59 | 60 | 2 | 33 | 5 | 30 | 3 | 0 |
subtype3 | 20 | 11 | 0 | 0 | 34 | 28 | 0 | 14 | 1 | 4 | 2 | 1 |
P value = 0.00011 (Fisher's exact test), Q value = 0.00034
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 184 | 379 | 85 | 19 |
subtype1 | 76 | 199 | 31 | 11 |
subtype2 | 60 | 122 | 46 | 5 |
subtype3 | 48 | 58 | 8 | 3 |
P value = 0.00022 (Fisher's exact test), Q value = 0.00065
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 318 | 229 | 67 | 45 |
subtype1 | 163 | 106 | 35 | 9 |
subtype2 | 100 | 76 | 23 | 31 |
subtype3 | 55 | 47 | 9 | 5 |
P value = 0.712 (Fisher's exact test), Q value = 0.79
nPatients | 0 | 1 |
---|---|---|
ALL | 516 | 8 |
subtype1 | 257 | 3 |
subtype2 | 161 | 3 |
subtype3 | 98 | 2 |
P value = 0.67 (Fisher's exact test), Q value = 0.77
nPatients | FEMALE | MALE |
---|---|---|
ALL | 659 | 9 |
subtype1 | 312 | 6 |
subtype2 | 231 | 2 |
subtype3 | 116 | 1 |
P value = 0.375 (Fisher's exact test), Q value = 0.47
nPatients | NO | YES |
---|---|---|
ALL | 282 | 337 |
subtype1 | 139 | 152 |
subtype2 | 102 | 123 |
subtype3 | 41 | 62 |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER, SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 436 | 161 | 5 | 9 | 16 | 15 | 25 |
subtype1 | 1 | 257 | 15 | 5 | 4 | 9 | 11 | 16 |
subtype2 | 0 | 91 | 127 | 0 | 5 | 2 | 3 | 5 |
subtype3 | 0 | 88 | 19 | 0 | 0 | 5 | 1 | 4 |
P value = 0.00554 (Kruskal-Wallis (anova)), Q value = 0.012
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 600 | 2.5 (5.0) |
subtype1 | 282 | 1.8 (3.9) |
subtype2 | 208 | 3.7 (6.7) |
subtype3 | 110 | 1.9 (3.5) |
P value = 1e-05 (Fisher's exact test), Q value = 5e-05
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 51 | 145 | 466 |
subtype1 | 26 | 80 | 210 |
subtype2 | 18 | 59 | 153 |
subtype3 | 7 | 6 | 103 |
P value = 0.821 (Fisher's exact test), Q value = 0.88
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 29 | 608 |
subtype1 | 14 | 289 |
subtype2 | 9 | 214 |
subtype3 | 6 | 105 |
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Cluster data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BRCA-TP/22595637/BRCA-TP.mergedcluster.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BRCA-TP/22506573/BRCA-TP.merged_data.txt
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Number of patients = 1097
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Number of clustering approaches = 12
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Number of selected clinical features = 12
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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.