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 10 clinical features across 975 patients, 43 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 8 subtypes that correlate to 'AGE', 'PATHOLOGY.N.STAGE', and 'HISTOLOGICAL.TYPE'.
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Consensus hierarchical clustering analysis on array-based mRNA expression data identified 3 subtypes that correlate to 'AGE' and 'HISTOLOGICAL.TYPE'.
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5 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes correlate to 'PATHOLOGY.T.STAGE', 'GENDER', and 'HISTOLOGICAL.TYPE'.
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6 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'AGE', 'PATHOLOGY.T.STAGE', and 'HISTOLOGICAL.TYPE'.
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CNMF clustering analysis on RPPA data identified 3 subtypes that correlate to 'PATHOLOGY.T.STAGE' and 'HISTOLOGICAL.TYPE'.
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Consensus hierarchical clustering analysis on RPPA data identified 3 subtypes that correlate to 'AGE' and 'HISTOLOGICAL.TYPE'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'AGE', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', 'PATHOLOGY.N.STAGE', and 'HISTOLOGICAL.TYPE'.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'AGE', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', and 'HISTOLOGICAL.TYPE'.
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3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', 'PATHOLOGY.N.STAGE', 'PATHOLOGY.M.STAGE', and 'HISTOLOGICAL.TYPE'.
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3 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes correlate to 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.N.STAGE', and 'HISTOLOGICAL.TYPE'.
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3 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes correlate to 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', 'PATHOLOGY.N.STAGE', 'PATHOLOGY.M.STAGE', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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3 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes correlate to 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.N.STAGE', 'PATHOLOGY.M.STAGE', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBER OF LYMPH NODES |
Statistical Tests | logrank test | ANOVA | Chi-square test | Chi-square test | Chi-square test | Chi-square test | Fisher's exact test | Chi-square test | Fisher's exact test | ANOVA |
mRNA CNMF subtypes |
0.0464 (1.00) |
2.59e-08 (2.9e-06) |
0.0268 (1.00) |
0.0413 (1.00) |
0.000806 (0.0693) |
0.54 (1.00) |
0.0459 (1.00) |
1.04e-05 (0.00107) |
0.307 (1.00) |
0.397 (1.00) |
mRNA cHierClus subtypes |
0.899 (1.00) |
0.000796 (0.0693) |
0.0805 (1.00) |
0.0433 (1.00) |
0.27 (1.00) |
0.143 (1.00) |
0.491 (1.00) |
1.22e-07 (1.35e-05) |
0.0214 (1.00) |
0.646 (1.00) |
Copy Number Ratio CNMF subtypes |
0.231 (1.00) |
0.0363 (1.00) |
0.0202 (1.00) |
3.59e-08 (3.99e-06) |
0.00699 (0.489) |
0.324 (1.00) |
0.000153 (0.0144) |
5.38e-18 (6.13e-16) |
0.236 (1.00) |
0.259 (1.00) |
METHLYATION CNMF |
0.443 (1.00) |
2.26e-05 (0.0023) |
0.034 (1.00) |
0.00304 (0.237) |
0.00563 (0.411) |
0.35 (1.00) |
0.0107 (0.709) |
4.18e-12 (4.72e-10) |
0.0254 (1.00) |
0.022 (1.00) |
RPPA CNMF subtypes |
0.0474 (1.00) |
0.0287 (1.00) |
0.0315 (1.00) |
0.00137 (0.113) |
0.163 (1.00) |
0.323 (1.00) |
0.0564 (1.00) |
0.000131 (0.0126) |
0.65 (1.00) |
0.0305 (1.00) |
RPPA cHierClus subtypes |
0.378 (1.00) |
0.00121 (0.1) |
0.0442 (1.00) |
0.00703 (0.489) |
0.738 (1.00) |
0.665 (1.00) |
0.154 (1.00) |
0.000479 (0.0426) |
0.421 (1.00) |
0.0553 (1.00) |
RNAseq CNMF subtypes |
0.047 (1.00) |
0.000373 (0.0336) |
3.87e-07 (4.22e-05) |
0.000232 (0.0216) |
0.00105 (0.0884) |
0.127 (1.00) |
0.0133 (0.863) |
1.07e-33 (1.26e-31) |
0.794 (1.00) |
0.0318 (1.00) |
RNAseq cHierClus subtypes |
0.00863 (0.578) |
7.11e-05 (0.00697) |
3.89e-06 (0.000404) |
8.37e-07 (8.96e-05) |
0.018 (1.00) |
0.0283 (1.00) |
0.0717 (1.00) |
9.92e-36 (1.18e-33) |
0.444 (1.00) |
0.282 (1.00) |
MIRSEQ CNMF |
0.0197 (1.00) |
0.187 (1.00) |
1.74e-06 (0.000183) |
9.76e-05 (0.00946) |
0.00272 (0.215) |
0.000336 (0.0309) |
0.474 (1.00) |
5.22e-44 (6.27e-42) |
0.00424 (0.327) |
0.0275 (1.00) |
MIRSEQ CHIERARCHICAL |
0.115 (1.00) |
0.0289 (1.00) |
0.00224 (0.179) |
0.00797 (0.542) |
3.54e-05 (0.0035) |
0.0162 (1.00) |
0.192 (1.00) |
5.58e-31 (6.41e-29) |
0.0045 (0.342) |
0.275 (1.00) |
MIRseq Mature CNMF subtypes |
0.00668 (0.475) |
0.19 (1.00) |
5.79e-07 (6.25e-05) |
8.69e-07 (9.21e-05) |
2.31e-05 (0.00234) |
0.00156 (0.127) |
0.348 (1.00) |
1.44e-31 (1.67e-29) |
0.000339 (0.0309) |
0.00538 (0.398) |
MIRseq Mature cHierClus subtypes |
0.00473 (0.355) |
0.0921 (1.00) |
0.000136 (0.0129) |
0.0066 (0.475) |
0.000966 (0.0821) |
0.000542 (0.0477) |
0.358 (1.00) |
8.86e-34 (1.05e-31) |
3.15e-05 (0.00315) |
0.0187 (1.00) |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 |
---|---|---|---|---|---|---|---|---|
Number of samples | 21 | 39 | 121 | 101 | 110 | 74 | 20 | 40 |
P value = 0.0464 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 496 | 72 | 0.1 - 234.2 (28.5) |
subtype1 | 19 | 3 | 0.3 - 92.0 (16.3) |
subtype2 | 38 | 3 | 0.1 - 157.4 (43.5) |
subtype3 | 112 | 18 | 0.1 - 188.7 (27.6) |
subtype4 | 96 | 13 | 0.2 - 211.5 (28.3) |
subtype5 | 107 | 11 | 0.3 - 234.2 (26.0) |
subtype6 | 66 | 15 | 0.2 - 189.0 (31.9) |
subtype7 | 19 | 3 | 0.2 - 97.5 (41.8) |
subtype8 | 39 | 6 | 0.3 - 112.4 (27.5) |
P value = 2.59e-08 (ANOVA), Q value = 2.9e-06
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 526 | 57.9 (13.2) |
subtype1 | 21 | 59.9 (13.8) |
subtype2 | 39 | 48.3 (10.6) |
subtype3 | 121 | 58.1 (14.2) |
subtype4 | 101 | 53.9 (12.5) |
subtype5 | 110 | 62.6 (12.5) |
subtype6 | 74 | 58.6 (12.5) |
subtype7 | 20 | 60.4 (9.9) |
subtype8 | 40 | 60.6 (12.0) |
P value = 0.0268 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 46 | 37 | 6 | 185 | 110 | 77 | 15 | 19 | 14 | 1 | 16 |
subtype1 | 1 | 0 | 0 | 8 | 3 | 5 | 1 | 0 | 2 | 0 | 1 |
subtype2 | 1 | 3 | 0 | 12 | 10 | 8 | 0 | 2 | 1 | 1 | 1 |
subtype3 | 8 | 6 | 4 | 36 | 34 | 20 | 6 | 3 | 1 | 0 | 3 |
subtype4 | 8 | 10 | 0 | 45 | 19 | 9 | 1 | 4 | 3 | 0 | 2 |
subtype5 | 14 | 14 | 0 | 43 | 15 | 10 | 5 | 2 | 3 | 0 | 4 |
subtype6 | 4 | 2 | 0 | 21 | 19 | 15 | 2 | 6 | 3 | 0 | 2 |
subtype7 | 4 | 1 | 0 | 6 | 4 | 4 | 0 | 0 | 0 | 0 | 1 |
subtype8 | 6 | 1 | 2 | 14 | 6 | 6 | 0 | 2 | 1 | 0 | 2 |
P value = 0.0413 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 133 | 311 | 59 | 20 |
subtype1 | 6 | 13 | 0 | 2 |
subtype2 | 8 | 21 | 9 | 0 |
subtype3 | 25 | 75 | 14 | 6 |
subtype4 | 23 | 67 | 8 | 2 |
subtype5 | 40 | 55 | 9 | 6 |
subtype6 | 11 | 49 | 12 | 2 |
subtype7 | 7 | 10 | 3 | 0 |
subtype8 | 13 | 21 | 4 | 2 |
P value = 0.000806 (Chi-square test), Q value = 0.069
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 255 | 170 | 61 | 29 |
subtype1 | 6 | 6 | 7 | 1 |
subtype2 | 14 | 16 | 5 | 3 |
subtype3 | 49 | 50 | 14 | 4 |
subtype4 | 64 | 24 | 8 | 5 |
subtype5 | 66 | 31 | 7 | 5 |
subtype6 | 24 | 26 | 14 | 8 |
subtype7 | 11 | 5 | 3 | 0 |
subtype8 | 21 | 12 | 3 | 3 |
P value = 0.54 (Chi-square test), Q value = 1
nPatients | CM0 (I+) | M0 | M1 | MX |
---|---|---|---|---|
ALL | 2 | 496 | 14 | 14 |
subtype1 | 0 | 19 | 2 | 0 |
subtype2 | 1 | 37 | 1 | 0 |
subtype3 | 0 | 116 | 1 | 4 |
subtype4 | 0 | 97 | 3 | 1 |
subtype5 | 1 | 101 | 3 | 5 |
subtype6 | 0 | 70 | 3 | 1 |
subtype7 | 0 | 19 | 0 | 1 |
subtype8 | 0 | 37 | 1 | 2 |
P value = 0.0459 (Chi-square test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 520 | 6 |
subtype1 | 20 | 1 |
subtype2 | 39 | 0 |
subtype3 | 117 | 4 |
subtype4 | 101 | 0 |
subtype5 | 110 | 0 |
subtype6 | 74 | 0 |
subtype7 | 19 | 1 |
subtype8 | 40 | 0 |
P value = 1.04e-05 (Chi-square test), Q value = 0.0011
nPatients | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|
ALL | 448 | 41 | 1 | 12 | 2 | 21 |
subtype1 | 20 | 0 | 0 | 0 | 0 | 1 |
subtype2 | 28 | 8 | 0 | 3 | 0 | 0 |
subtype3 | 113 | 1 | 0 | 1 | 1 | 5 |
subtype4 | 92 | 1 | 1 | 0 | 0 | 6 |
subtype5 | 85 | 14 | 0 | 5 | 1 | 5 |
subtype6 | 67 | 5 | 0 | 0 | 0 | 2 |
subtype7 | 19 | 1 | 0 | 0 | 0 | 0 |
subtype8 | 24 | 11 | 0 | 3 | 0 | 2 |
P value = 0.307 (Chi-square test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 168 | 358 |
subtype1 | 3 | 18 |
subtype2 | 14 | 25 |
subtype3 | 35 | 86 |
subtype4 | 41 | 60 |
subtype5 | 33 | 77 |
subtype6 | 22 | 52 |
subtype7 | 8 | 12 |
subtype8 | 12 | 28 |
P value = 0.397 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 406 | 1.8 (3.5) |
subtype1 | 14 | 1.4 (2.2) |
subtype2 | 34 | 1.9 (2.4) |
subtype3 | 86 | 1.6 (2.3) |
subtype4 | 92 | 1.4 (3.2) |
subtype5 | 84 | 1.8 (3.9) |
subtype6 | 46 | 2.8 (3.5) |
subtype7 | 15 | 1.2 (2.5) |
subtype8 | 35 | 2.7 (6.3) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 124 | 131 | 271 |
P value = 0.899 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 496 | 72 | 0.1 - 234.2 (28.5) |
subtype1 | 122 | 15 | 0.3 - 157.4 (31.5) |
subtype2 | 121 | 20 | 0.3 - 211.5 (31.8) |
subtype3 | 253 | 37 | 0.1 - 234.2 (25.2) |
P value = 0.000796 (ANOVA), Q value = 0.069
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 526 | 57.9 (13.2) |
subtype1 | 124 | 56.4 (13.0) |
subtype2 | 131 | 55.1 (13.1) |
subtype3 | 271 | 60.0 (13.1) |
P value = 0.0805 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 46 | 37 | 6 | 185 | 110 | 77 | 15 | 19 | 14 | 1 | 16 |
subtype1 | 18 | 9 | 2 | 38 | 22 | 21 | 1 | 5 | 2 | 1 | 5 |
subtype2 | 9 | 11 | 0 | 56 | 25 | 13 | 2 | 8 | 4 | 0 | 3 |
subtype3 | 19 | 17 | 4 | 91 | 63 | 43 | 12 | 6 | 8 | 0 | 8 |
P value = 0.0433 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 133 | 311 | 59 | 20 |
subtype1 | 43 | 60 | 17 | 3 |
subtype2 | 30 | 85 | 12 | 3 |
subtype3 | 60 | 166 | 30 | 14 |
P value = 0.27 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 255 | 170 | 61 | 29 |
subtype1 | 62 | 37 | 14 | 8 |
subtype2 | 74 | 34 | 14 | 9 |
subtype3 | 119 | 99 | 33 | 12 |
P value = 0.143 (Chi-square test), Q value = 1
nPatients | CM0 (I+) | M0 | M1 | MX |
---|---|---|---|---|
ALL | 2 | 496 | 14 | 14 |
subtype1 | 2 | 116 | 2 | 4 |
subtype2 | 0 | 126 | 4 | 1 |
subtype3 | 0 | 254 | 8 | 9 |
P value = 0.491 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 520 | 6 |
subtype1 | 122 | 2 |
subtype2 | 131 | 0 |
subtype3 | 267 | 4 |
P value = 1.22e-07 (Chi-square test), Q value = 1.3e-05
nPatients | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|
ALL | 448 | 41 | 1 | 12 | 2 | 21 |
subtype1 | 88 | 26 | 0 | 6 | 0 | 4 |
subtype2 | 119 | 4 | 1 | 0 | 0 | 6 |
subtype3 | 241 | 11 | 0 | 6 | 2 | 11 |
P value = 0.0214 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 168 | 358 |
subtype1 | 42 | 82 |
subtype2 | 53 | 78 |
subtype3 | 73 | 198 |
P value = 0.646 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 406 | 1.8 (3.5) |
subtype1 | 110 | 2.1 (4.2) |
subtype2 | 114 | 1.7 (3.3) |
subtype3 | 182 | 1.7 (3.2) |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 355 | 248 | 87 | 224 | 43 |
P value = 0.231 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 920 | 110 | 0.0 - 234.2 (21.6) |
subtype1 | 342 | 36 | 0.0 - 234.2 (24.1) |
subtype2 | 234 | 29 | 0.1 - 162.0 (21.3) |
subtype3 | 86 | 8 | 0.0 - 189.0 (18.2) |
subtype4 | 216 | 28 | 0.2 - 211.5 (22.8) |
subtype5 | 42 | 9 | 0.2 - 220.9 (21.9) |
P value = 0.0363 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 954 | 58.6 (13.2) |
subtype1 | 353 | 58.9 (13.1) |
subtype2 | 248 | 58.7 (14.0) |
subtype3 | 87 | 60.6 (12.4) |
subtype4 | 224 | 56.5 (12.7) |
subtype5 | 42 | 61.7 (12.6) |
P value = 0.0202 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 77 | 73 | 9 | 9 | 321 | 217 | 2 | 135 | 27 | 54 | 15 | 1 | 16 |
subtype1 | 38 | 42 | 6 | 7 | 100 | 74 | 1 | 43 | 8 | 23 | 4 | 0 | 9 |
subtype2 | 12 | 13 | 2 | 1 | 83 | 56 | 1 | 46 | 13 | 12 | 6 | 0 | 3 |
subtype3 | 5 | 2 | 0 | 1 | 28 | 25 | 0 | 12 | 3 | 8 | 2 | 0 | 1 |
subtype4 | 18 | 14 | 1 | 0 | 92 | 52 | 0 | 27 | 3 | 9 | 3 | 1 | 3 |
subtype5 | 4 | 2 | 0 | 0 | 18 | 10 | 0 | 7 | 0 | 2 | 0 | 0 | 0 |
P value = 3.59e-08 (Chi-square test), Q value = 4e-06
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 248 | 556 | 114 | 36 |
subtype1 | 131 | 159 | 52 | 12 |
subtype2 | 48 | 163 | 24 | 13 |
subtype3 | 10 | 59 | 13 | 5 |
subtype4 | 45 | 151 | 21 | 5 |
subtype5 | 14 | 24 | 4 | 1 |
P value = 0.00699 (Chi-square test), Q value = 0.49
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 448 | 320 | 109 | 65 |
subtype1 | 174 | 118 | 29 | 27 |
subtype2 | 94 | 91 | 40 | 16 |
subtype3 | 36 | 32 | 8 | 10 |
subtype4 | 126 | 62 | 26 | 10 |
subtype5 | 18 | 17 | 6 | 2 |
P value = 0.324 (Chi-square test), Q value = 1
nPatients | CM0 (I+) | M0 | M1 | MX |
---|---|---|---|---|
ALL | 2 | 825 | 15 | 115 |
subtype1 | 1 | 293 | 4 | 57 |
subtype2 | 1 | 218 | 6 | 23 |
subtype3 | 0 | 74 | 2 | 11 |
subtype4 | 0 | 200 | 3 | 21 |
subtype5 | 0 | 40 | 0 | 3 |
P value = 0.000153 (Chi-square test), Q value = 0.014
nPatients | FEMALE | MALE |
---|---|---|
ALL | 947 | 10 |
subtype1 | 355 | 0 |
subtype2 | 239 | 9 |
subtype3 | 86 | 1 |
subtype4 | 224 | 0 |
subtype5 | 43 | 0 |
P value = 5.38e-18 (Chi-square test), Q value = 6.1e-16
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
subtype1 | 0 | 214 | 94 | 0 | 15 | 10 | 22 |
subtype2 | 0 | 213 | 22 | 0 | 3 | 2 | 8 |
subtype3 | 0 | 54 | 27 | 0 | 5 | 0 | 1 |
subtype4 | 1 | 200 | 4 | 4 | 4 | 0 | 10 |
subtype5 | 0 | 29 | 7 | 1 | 1 | 2 | 3 |
P value = 0.236 (Chi-square test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 281 | 676 |
subtype1 | 94 | 261 |
subtype2 | 75 | 173 |
subtype3 | 21 | 66 |
subtype4 | 76 | 148 |
subtype5 | 15 | 28 |
P value = 0.259 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 797 | 2.3 (4.6) |
subtype1 | 307 | 2.2 (4.5) |
subtype2 | 183 | 2.6 (4.1) |
subtype3 | 71 | 3.3 (5.6) |
subtype4 | 197 | 1.9 (4.9) |
subtype5 | 39 | 2.5 (4.4) |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 108 | 153 | 101 | 135 | 50 | 105 |
P value = 0.443 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 644 | 72 | 0.0 - 234.2 (21.2) |
subtype1 | 108 | 17 | 0.2 - 211.5 (21.9) |
subtype2 | 150 | 14 | 0.3 - 234.2 (18.1) |
subtype3 | 101 | 13 | 0.0 - 130.1 (18.2) |
subtype4 | 134 | 14 | 0.1 - 194.3 (23.8) |
subtype5 | 47 | 5 | 0.1 - 157.4 (21.0) |
subtype6 | 104 | 9 | 0.0 - 130.2 (27.6) |
P value = 2.26e-05 (ANOVA), Q value = 0.0023
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 649 | 58.0 (13.1) |
subtype1 | 107 | 55.4 (12.7) |
subtype2 | 152 | 58.7 (12.3) |
subtype3 | 101 | 63.8 (11.5) |
subtype4 | 135 | 56.0 (14.5) |
subtype5 | 50 | 57.6 (14.1) |
subtype6 | 104 | 56.6 (12.2) |
P value = 0.034 (Chi-square test), Q value = 1
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 | 49 | 54 | 5 | 8 | 206 | 152 | 2 | 106 | 17 | 41 | 6 | 5 |
subtype1 | 5 | 6 | 0 | 0 | 49 | 28 | 0 | 12 | 1 | 3 | 2 | 1 |
subtype2 | 10 | 13 | 1 | 3 | 43 | 45 | 0 | 21 | 4 | 11 | 0 | 2 |
subtype3 | 7 | 5 | 0 | 2 | 30 | 22 | 1 | 21 | 2 | 8 | 2 | 1 |
subtype4 | 8 | 11 | 2 | 0 | 36 | 36 | 0 | 27 | 7 | 6 | 1 | 1 |
subtype5 | 3 | 7 | 0 | 1 | 14 | 5 | 0 | 10 | 2 | 7 | 1 | 0 |
subtype6 | 16 | 12 | 2 | 2 | 34 | 16 | 1 | 15 | 1 | 6 | 0 | 0 |
P value = 0.00304 (Chi-square test), Q value = 0.24
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 173 | 372 | 85 | 20 |
subtype1 | 18 | 74 | 12 | 3 |
subtype2 | 42 | 86 | 21 | 3 |
subtype3 | 18 | 62 | 18 | 3 |
subtype4 | 34 | 78 | 15 | 8 |
subtype5 | 15 | 25 | 8 | 2 |
subtype6 | 46 | 47 | 11 | 1 |
P value = 0.00563 (Chi-square test), Q value = 0.41
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 285 | 231 | 84 | 44 |
subtype1 | 62 | 31 | 11 | 4 |
subtype2 | 58 | 66 | 15 | 11 |
subtype3 | 47 | 25 | 19 | 8 |
subtype4 | 46 | 59 | 21 | 7 |
subtype5 | 19 | 16 | 7 | 7 |
subtype6 | 53 | 34 | 11 | 7 |
P value = 0.35 (Chi-square test), Q value = 1
nPatients | CM0 (I+) | M0 | M1 | MX |
---|---|---|---|---|
ALL | 1 | 541 | 6 | 104 |
subtype1 | 0 | 94 | 2 | 12 |
subtype2 | 1 | 127 | 0 | 25 |
subtype3 | 0 | 76 | 2 | 23 |
subtype4 | 0 | 118 | 1 | 16 |
subtype5 | 0 | 41 | 1 | 8 |
subtype6 | 0 | 85 | 0 | 20 |
P value = 0.0107 (Chi-square test), Q value = 0.71
nPatients | FEMALE | MALE |
---|---|---|
ALL | 645 | 7 |
subtype1 | 108 | 0 |
subtype2 | 152 | 1 |
subtype3 | 99 | 2 |
subtype4 | 134 | 1 |
subtype5 | 47 | 3 |
subtype6 | 105 | 0 |
P value = 4.18e-12 (Chi-square test), Q value = 4.7e-10
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 447 | 131 | 5 | 23 | 12 | 32 |
subtype1 | 1 | 87 | 3 | 3 | 1 | 0 | 12 |
subtype2 | 0 | 79 | 48 | 0 | 12 | 5 | 9 |
subtype3 | 0 | 64 | 32 | 0 | 3 | 0 | 2 |
subtype4 | 0 | 115 | 7 | 0 | 3 | 4 | 6 |
subtype5 | 0 | 35 | 10 | 0 | 2 | 2 | 1 |
subtype6 | 0 | 67 | 31 | 2 | 2 | 1 | 2 |
P value = 0.0254 (Chi-square test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 214 | 438 |
subtype1 | 42 | 66 |
subtype2 | 42 | 111 |
subtype3 | 29 | 72 |
subtype4 | 58 | 77 |
subtype5 | 13 | 37 |
subtype6 | 30 | 75 |
P value = 0.022 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 599 | 2.6 (4.8) |
subtype1 | 103 | 1.7 (3.1) |
subtype2 | 147 | 2.6 (4.7) |
subtype3 | 91 | 3.2 (6.0) |
subtype4 | 116 | 2.7 (4.4) |
subtype5 | 44 | 4.5 (6.8) |
subtype6 | 98 | 2.0 (4.4) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 152 | 136 | 120 |
P value = 0.0474 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 381 | 51 | 0.2 - 189.0 (29.9) |
subtype1 | 136 | 25 | 0.2 - 186.4 (30.0) |
subtype2 | 132 | 13 | 0.2 - 146.5 (25.8) |
subtype3 | 113 | 13 | 0.3 - 189.0 (34.2) |
P value = 0.0287 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 408 | 57.9 (13.1) |
subtype1 | 152 | 56.1 (13.4) |
subtype2 | 136 | 60.1 (13.7) |
subtype3 | 120 | 57.5 (11.7) |
P value = 0.0315 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 31 | 30 | 4 | 137 | 94 | 62 | 13 | 15 | 14 | 8 |
subtype1 | 6 | 8 | 0 | 55 | 36 | 24 | 2 | 10 | 8 | 3 |
subtype2 | 12 | 12 | 1 | 46 | 38 | 14 | 6 | 1 | 3 | 3 |
subtype3 | 13 | 10 | 3 | 36 | 20 | 24 | 5 | 4 | 3 | 2 |
P value = 0.00137 (Chi-square test), Q value = 0.11
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 93 | 246 | 50 | 18 |
subtype1 | 20 | 106 | 22 | 4 |
subtype2 | 35 | 83 | 11 | 6 |
subtype3 | 38 | 57 | 17 | 8 |
P value = 0.163 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 192 | 132 | 52 | 25 |
subtype1 | 70 | 45 | 22 | 12 |
subtype2 | 65 | 53 | 10 | 6 |
subtype3 | 57 | 34 | 20 | 7 |
P value = 0.323 (Chi-square test), Q value = 1
nPatients | CM0 (I+) | M0 | M1 | MX |
---|---|---|---|---|
ALL | 1 | 386 | 14 | 7 |
subtype1 | 0 | 143 | 8 | 1 |
subtype2 | 0 | 129 | 3 | 4 |
subtype3 | 1 | 114 | 3 | 2 |
P value = 0.0564 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 403 | 5 |
subtype1 | 152 | 0 |
subtype2 | 132 | 4 |
subtype3 | 119 | 1 |
P value = 0.000131 (Chi-square test), Q value = 0.013
nPatients | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|
ALL | 353 | 30 | 1 | 8 | 2 | 14 |
subtype1 | 139 | 4 | 1 | 1 | 0 | 7 |
subtype2 | 120 | 5 | 0 | 4 | 2 | 5 |
subtype3 | 94 | 21 | 0 | 3 | 0 | 2 |
P value = 0.65 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 144 | 264 |
subtype1 | 57 | 95 |
subtype2 | 44 | 92 |
subtype3 | 43 | 77 |
P value = 0.0305 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 330 | 1.9 (3.5) |
subtype1 | 114 | 2.1 (3.6) |
subtype2 | 113 | 1.2 (2.0) |
subtype3 | 103 | 2.4 (4.5) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 163 | 115 | 130 |
P value = 0.378 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 381 | 51 | 0.2 - 189.0 (29.9) |
subtype1 | 152 | 20 | 0.2 - 129.7 (28.2) |
subtype2 | 112 | 12 | 0.2 - 173.0 (31.4) |
subtype3 | 117 | 19 | 0.2 - 189.0 (31.7) |
P value = 0.00121 (ANOVA), Q value = 0.1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 408 | 57.9 (13.1) |
subtype1 | 163 | 60.4 (13.6) |
subtype2 | 115 | 57.6 (11.8) |
subtype3 | 130 | 54.8 (13.0) |
P value = 0.0442 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 31 | 30 | 4 | 137 | 94 | 62 | 13 | 15 | 14 | 8 |
subtype1 | 15 | 11 | 1 | 52 | 42 | 23 | 7 | 2 | 6 | 4 |
subtype2 | 11 | 12 | 3 | 31 | 21 | 23 | 5 | 4 | 3 | 2 |
subtype3 | 5 | 7 | 0 | 54 | 31 | 16 | 1 | 9 | 5 | 2 |
P value = 0.00703 (Chi-square test), Q value = 0.49
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 93 | 246 | 50 | 18 |
subtype1 | 36 | 101 | 18 | 7 |
subtype2 | 37 | 53 | 17 | 8 |
subtype3 | 20 | 92 | 15 | 3 |
P value = 0.738 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 192 | 132 | 52 | 25 |
subtype1 | 78 | 55 | 19 | 7 |
subtype2 | 51 | 37 | 18 | 7 |
subtype3 | 63 | 40 | 15 | 11 |
P value = 0.665 (Chi-square test), Q value = 1
nPatients | CM0 (I+) | M0 | M1 | MX |
---|---|---|---|---|
ALL | 1 | 386 | 14 | 7 |
subtype1 | 0 | 153 | 6 | 4 |
subtype2 | 1 | 109 | 3 | 2 |
subtype3 | 0 | 124 | 5 | 1 |
P value = 0.154 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 403 | 5 |
subtype1 | 159 | 4 |
subtype2 | 114 | 1 |
subtype3 | 130 | 0 |
P value = 0.000479 (Chi-square test), Q value = 0.043
nPatients | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|
ALL | 353 | 30 | 1 | 8 | 2 | 14 |
subtype1 | 143 | 8 | 0 | 5 | 2 | 5 |
subtype2 | 91 | 19 | 0 | 3 | 0 | 2 |
subtype3 | 119 | 3 | 1 | 0 | 0 | 7 |
P value = 0.421 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 144 | 264 |
subtype1 | 52 | 111 |
subtype2 | 41 | 74 |
subtype3 | 51 | 79 |
P value = 0.0553 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 330 | 1.9 (3.5) |
subtype1 | 126 | 1.3 (2.1) |
subtype2 | 99 | 2.4 (4.5) |
subtype3 | 105 | 2.1 (3.7) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 264 | 181 | 524 |
P value = 0.047 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 932 | 113 | 0.0 - 234.2 (21.8) |
subtype1 | 252 | 40 | 0.0 - 211.5 (23.2) |
subtype2 | 180 | 14 | 0.0 - 194.3 (28.0) |
subtype3 | 500 | 59 | 0.0 - 234.2 (20.5) |
P value = 0.000373 (ANOVA), Q value = 0.034
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 966 | 58.5 (13.2) |
subtype1 | 263 | 56.5 (12.4) |
subtype2 | 180 | 57.0 (12.5) |
subtype3 | 523 | 60.1 (13.6) |
P value = 3.87e-07 (Chi-square test), Q value = 4.2e-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 TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 78 | 75 | 10 | 9 | 326 | 221 | 2 | 134 | 27 | 53 | 15 | 1 | 17 |
subtype1 | 15 | 19 | 1 | 1 | 113 | 59 | 1 | 30 | 4 | 12 | 4 | 0 | 4 |
subtype2 | 21 | 18 | 3 | 7 | 40 | 42 | 0 | 22 | 1 | 21 | 2 | 1 | 3 |
subtype3 | 42 | 38 | 6 | 1 | 173 | 120 | 1 | 82 | 22 | 20 | 9 | 0 | 10 |
P value = 0.000232 (Chi-square test), Q value = 0.022
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 254 | 561 | 115 | 36 |
subtype1 | 58 | 168 | 29 | 8 |
subtype2 | 60 | 84 | 34 | 2 |
subtype3 | 136 | 309 | 52 | 26 |
P value = 0.00105 (Chi-square test), Q value = 0.088
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 456 | 325 | 108 | 64 |
subtype1 | 141 | 83 | 24 | 14 |
subtype2 | 82 | 61 | 13 | 23 |
subtype3 | 233 | 181 | 71 | 27 |
P value = 0.127 (Chi-square test), Q value = 1
nPatients | CM0 (I+) | M0 | M1 | MX |
---|---|---|---|---|
ALL | 2 | 837 | 15 | 115 |
subtype1 | 0 | 236 | 4 | 24 |
subtype2 | 1 | 146 | 2 | 32 |
subtype3 | 1 | 455 | 9 | 59 |
P value = 0.0133 (Fisher's exact test), Q value = 0.86
nPatients | FEMALE | MALE |
---|---|---|
ALL | 959 | 10 |
subtype1 | 264 | 0 |
subtype2 | 181 | 0 |
subtype3 | 514 | 10 |
P value = 1.07e-33 (Chi-square test), Q value = 1.3e-31
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 722 | 155 | 5 | 28 | 14 | 43 |
subtype1 | 1 | 231 | 7 | 5 | 2 | 0 | 17 |
subtype2 | 0 | 88 | 81 | 0 | 9 | 1 | 2 |
subtype3 | 0 | 403 | 67 | 0 | 17 | 13 | 24 |
P value = 0.794 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 282 | 687 |
subtype1 | 81 | 183 |
subtype2 | 51 | 130 |
subtype3 | 150 | 374 |
P value = 0.0318 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 807 | 2.3 (4.6) |
subtype1 | 224 | 2.2 (4.9) |
subtype2 | 166 | 3.1 (5.9) |
subtype3 | 417 | 2.1 (3.7) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 222 | 433 | 314 |
P value = 0.00863 (logrank test), Q value = 0.58
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 932 | 113 | 0.0 - 234.2 (21.8) |
subtype1 | 213 | 32 | 0.0 - 211.5 (22.0) |
subtype2 | 407 | 56 | 0.0 - 234.2 (20.4) |
subtype3 | 312 | 25 | 0.0 - 194.3 (27.2) |
P value = 7.11e-05 (ANOVA), Q value = 0.007
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 966 | 58.5 (13.2) |
subtype1 | 221 | 56.4 (12.6) |
subtype2 | 433 | 60.6 (13.8) |
subtype3 | 312 | 57.2 (12.3) |
P value = 3.89e-06 (Chi-square test), Q value = 4e-04
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 78 | 75 | 10 | 9 | 326 | 221 | 2 | 134 | 27 | 53 | 15 | 1 | 17 |
subtype1 | 14 | 18 | 1 | 0 | 100 | 46 | 1 | 22 | 2 | 11 | 3 | 0 | 3 |
subtype2 | 29 | 26 | 5 | 2 | 142 | 105 | 1 | 65 | 24 | 17 | 9 | 0 | 8 |
subtype3 | 35 | 31 | 4 | 7 | 84 | 70 | 0 | 47 | 1 | 25 | 3 | 1 | 6 |
P value = 8.37e-07 (Chi-square test), Q value = 9e-05
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 254 | 561 | 115 | 36 |
subtype1 | 54 | 140 | 22 | 5 |
subtype2 | 96 | 266 | 42 | 28 |
subtype3 | 104 | 155 | 51 | 3 |
P value = 0.018 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 456 | 325 | 108 | 64 |
subtype1 | 127 | 62 | 20 | 13 |
subtype2 | 184 | 156 | 57 | 24 |
subtype3 | 145 | 107 | 31 | 27 |
P value = 0.0283 (Chi-square test), Q value = 1
nPatients | CM0 (I+) | M0 | M1 | MX |
---|---|---|---|---|
ALL | 2 | 837 | 15 | 115 |
subtype1 | 0 | 201 | 3 | 18 |
subtype2 | 0 | 377 | 9 | 47 |
subtype3 | 2 | 259 | 3 | 50 |
P value = 0.0717 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 959 | 10 |
subtype1 | 222 | 0 |
subtype2 | 425 | 8 |
subtype3 | 312 | 2 |
P value = 9.92e-36 (Chi-square test), Q value = 1.2e-33
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 722 | 155 | 5 | 28 | 14 | 43 |
subtype1 | 1 | 193 | 5 | 4 | 2 | 0 | 16 |
subtype2 | 0 | 355 | 32 | 0 | 14 | 13 | 19 |
subtype3 | 0 | 174 | 118 | 1 | 12 | 1 | 8 |
P value = 0.444 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 282 | 687 |
subtype1 | 72 | 150 |
subtype2 | 120 | 313 |
subtype3 | 90 | 224 |
P value = 0.282 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 807 | 2.3 (4.6) |
subtype1 | 192 | 2.0 (4.7) |
subtype2 | 328 | 2.2 (3.8) |
subtype3 | 287 | 2.6 (5.2) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 407 | 266 | 281 |
P value = 0.0197 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 917 | 110 | 0.0 - 234.2 (21.6) |
subtype1 | 384 | 49 | 0.0 - 234.2 (22.6) |
subtype2 | 264 | 20 | 0.0 - 194.3 (20.7) |
subtype3 | 269 | 41 | 0.0 - 211.5 (21.5) |
P value = 0.187 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 951 | 58.6 (13.2) |
subtype1 | 407 | 59.2 (13.6) |
subtype2 | 264 | 58.8 (12.5) |
subtype3 | 280 | 57.4 (13.3) |
P value = 1.74e-06 (Chi-square test), Q value = 0.00018
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 77 | 75 | 10 | 9 | 321 | 216 | 2 | 132 | 26 | 53 | 14 | 1 | 17 |
subtype1 | 37 | 32 | 3 | 1 | 131 | 96 | 1 | 60 | 14 | 14 | 9 | 0 | 9 |
subtype2 | 23 | 28 | 6 | 8 | 65 | 61 | 1 | 36 | 7 | 27 | 1 | 0 | 3 |
subtype3 | 17 | 15 | 1 | 0 | 125 | 59 | 0 | 36 | 5 | 12 | 4 | 1 | 5 |
P value = 9.76e-05 (Chi-square test), Q value = 0.0095
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 253 | 550 | 112 | 36 |
subtype1 | 117 | 232 | 39 | 19 |
subtype2 | 82 | 129 | 46 | 8 |
subtype3 | 54 | 189 | 27 | 9 |
P value = 0.00272 (Chi-square test), Q value = 0.22
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 450 | 319 | 106 | 63 |
subtype1 | 178 | 148 | 52 | 20 |
subtype2 | 119 | 91 | 24 | 29 |
subtype3 | 153 | 80 | 30 | 14 |
P value = 0.000336 (Chi-square test), Q value = 0.031
nPatients | CM0 (I+) | M0 | M1 | MX |
---|---|---|---|---|
ALL | 2 | 822 | 14 | 116 |
subtype1 | 1 | 361 | 9 | 36 |
subtype2 | 1 | 211 | 1 | 53 |
subtype3 | 0 | 250 | 4 | 27 |
P value = 0.474 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 944 | 10 |
subtype1 | 401 | 6 |
subtype2 | 265 | 1 |
subtype3 | 278 | 3 |
P value = 5.22e-44 (Chi-square test), Q value = 6.3e-42
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 709 | 153 | 5 | 27 | 14 | 44 |
subtype1 | 0 | 335 | 29 | 0 | 16 | 4 | 23 |
subtype2 | 0 | 132 | 117 | 0 | 7 | 5 | 5 |
subtype3 | 1 | 242 | 7 | 5 | 4 | 5 | 16 |
P value = 0.00424 (Fisher's exact test), Q value = 0.33
nPatients | NO | YES |
---|---|---|
ALL | 277 | 677 |
subtype1 | 133 | 274 |
subtype2 | 57 | 209 |
subtype3 | 87 | 194 |
P value = 0.0275 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 798 | 2.3 (4.6) |
subtype1 | 326 | 2.1 (3.7) |
subtype2 | 236 | 3.0 (5.7) |
subtype3 | 236 | 2.0 (4.3) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 242 | 302 | 410 |
P value = 0.115 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 917 | 110 | 0.0 - 234.2 (21.6) |
subtype1 | 233 | 38 | 0.0 - 211.5 (23.7) |
subtype2 | 281 | 32 | 0.1 - 234.2 (21.9) |
subtype3 | 403 | 40 | 0.0 - 189.0 (20.9) |
P value = 0.0289 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 951 | 58.6 (13.2) |
subtype1 | 241 | 56.6 (12.5) |
subtype2 | 302 | 59.5 (14.4) |
subtype3 | 408 | 59.0 (12.6) |
P value = 0.00224 (Chi-square test), Q value = 0.18
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 77 | 75 | 10 | 9 | 321 | 216 | 2 | 132 | 26 | 53 | 14 | 1 | 17 |
subtype1 | 15 | 17 | 1 | 1 | 104 | 50 | 0 | 29 | 3 | 12 | 5 | 0 | 4 |
subtype2 | 20 | 20 | 3 | 0 | 95 | 75 | 0 | 56 | 14 | 11 | 3 | 0 | 5 |
subtype3 | 42 | 38 | 6 | 8 | 122 | 91 | 2 | 47 | 9 | 30 | 6 | 1 | 8 |
P value = 0.00797 (Chi-square test), Q value = 0.54
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 253 | 550 | 112 | 36 |
subtype1 | 53 | 159 | 23 | 6 |
subtype2 | 72 | 180 | 33 | 16 |
subtype3 | 128 | 211 | 56 | 14 |
P value = 3.54e-05 (Chi-square test), Q value = 0.0035
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 450 | 319 | 106 | 63 |
subtype1 | 137 | 62 | 27 | 13 |
subtype2 | 116 | 118 | 46 | 14 |
subtype3 | 197 | 139 | 33 | 36 |
P value = 0.0162 (Chi-square test), Q value = 1
nPatients | CM0 (I+) | M0 | M1 | MX |
---|---|---|---|---|
ALL | 2 | 822 | 14 | 116 |
subtype1 | 0 | 213 | 5 | 24 |
subtype2 | 1 | 274 | 3 | 24 |
subtype3 | 1 | 335 | 6 | 68 |
P value = 0.192 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 944 | 10 |
subtype1 | 241 | 1 |
subtype2 | 296 | 6 |
subtype3 | 407 | 3 |
P value = 5.58e-31 (Chi-square test), Q value = 6.4e-29
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 709 | 153 | 5 | 27 | 14 | 44 |
subtype1 | 1 | 212 | 7 | 4 | 2 | 0 | 15 |
subtype2 | 0 | 252 | 13 | 0 | 12 | 11 | 14 |
subtype3 | 0 | 245 | 133 | 1 | 13 | 3 | 15 |
P value = 0.0045 (Fisher's exact test), Q value = 0.34
nPatients | NO | YES |
---|---|---|
ALL | 277 | 677 |
subtype1 | 76 | 166 |
subtype2 | 104 | 198 |
subtype3 | 97 | 313 |
P value = 0.275 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 798 | 2.3 (4.6) |
subtype1 | 206 | 2.0 (4.3) |
subtype2 | 233 | 2.2 (3.5) |
subtype3 | 359 | 2.6 (5.2) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 252 | 198 | 183 |
P value = 0.00668 (logrank test), Q value = 0.48
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 605 | 72 | 0.0 - 194.3 (20.4) |
subtype1 | 239 | 33 | 0.1 - 189.0 (21.6) |
subtype2 | 194 | 14 | 0.0 - 194.3 (18.3) |
subtype3 | 172 | 25 | 0.0 - 130.2 (20.2) |
P value = 0.19 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 630 | 58.3 (13.1) |
subtype1 | 252 | 57.3 (13.6) |
subtype2 | 196 | 59.6 (12.6) |
subtype3 | 182 | 58.1 (12.9) |
P value = 5.79e-07 (Chi-square test), Q value = 6.3e-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 | 67 | 47 | 5 | 9 | 212 | 146 | 2 | 85 | 13 | 38 | 3 | 5 |
subtype1 | 33 | 23 | 1 | 2 | 85 | 58 | 0 | 34 | 6 | 6 | 2 | 2 |
subtype2 | 19 | 17 | 4 | 7 | 42 | 52 | 2 | 26 | 4 | 24 | 1 | 0 |
subtype3 | 15 | 7 | 0 | 0 | 85 | 36 | 0 | 25 | 3 | 8 | 0 | 3 |
P value = 8.69e-07 (Chi-square test), Q value = 9.2e-05
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 187 | 353 | 74 | 19 |
subtype1 | 96 | 130 | 17 | 9 |
subtype2 | 55 | 99 | 40 | 4 |
subtype3 | 36 | 124 | 17 | 6 |
P value = 2.31e-05 (Chi-square test), Q value = 0.0023
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 300 | 221 | 65 | 40 |
subtype1 | 116 | 98 | 27 | 7 |
subtype2 | 80 | 75 | 16 | 25 |
subtype3 | 104 | 48 | 22 | 8 |
P value = 0.00156 (Chi-square test), Q value = 0.13
nPatients | CM0 (I+) | M0 | M1 | MX |
---|---|---|---|---|
ALL | 2 | 523 | 3 | 105 |
subtype1 | 2 | 221 | 2 | 27 |
subtype2 | 0 | 147 | 1 | 50 |
subtype3 | 0 | 155 | 0 | 28 |
P value = 0.348 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 626 | 7 |
subtype1 | 247 | 5 |
subtype2 | 197 | 1 |
subtype3 | 182 | 1 |
P value = 1.44e-31 (Chi-square test), Q value = 1.7e-29
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 439 | 127 | 5 | 18 | 14 | 29 |
subtype1 | 0 | 201 | 21 | 0 | 13 | 5 | 12 |
subtype2 | 0 | 87 | 97 | 0 | 4 | 6 | 4 |
subtype3 | 1 | 151 | 9 | 5 | 1 | 3 | 13 |
P value = 0.000339 (Fisher's exact test), Q value = 0.031
nPatients | NO | YES |
---|---|---|
ALL | 173 | 460 |
subtype1 | 83 | 169 |
subtype2 | 34 | 164 |
subtype3 | 56 | 127 |
P value = 0.00538 (ANOVA), Q value = 0.4
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 562 | 2.5 (5.0) |
subtype1 | 230 | 1.9 (3.7) |
subtype2 | 177 | 3.5 (6.1) |
subtype3 | 155 | 2.3 (5.0) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 133 | 157 | 343 |
P value = 0.00473 (logrank test), Q value = 0.35
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 605 | 72 | 0.0 - 194.3 (20.4) |
subtype1 | 129 | 20 | 0.2 - 114.1 (22.0) |
subtype2 | 156 | 8 | 0.0 - 194.3 (16.9) |
subtype3 | 320 | 44 | 0.0 - 189.0 (21.5) |
P value = 0.0921 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 630 | 58.3 (13.1) |
subtype1 | 132 | 57.6 (12.9) |
subtype2 | 156 | 60.2 (13.2) |
subtype3 | 342 | 57.6 (13.1) |
P value = 0.000136 (Chi-square test), Q value = 0.013
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 | 67 | 47 | 5 | 9 | 212 | 146 | 2 | 85 | 13 | 38 | 3 | 5 |
subtype1 | 13 | 6 | 1 | 0 | 59 | 29 | 0 | 13 | 2 | 8 | 0 | 1 |
subtype2 | 11 | 13 | 2 | 7 | 37 | 40 | 2 | 21 | 4 | 19 | 1 | 0 |
subtype3 | 43 | 28 | 2 | 2 | 116 | 77 | 0 | 51 | 7 | 11 | 2 | 4 |
P value = 0.0066 (Chi-square test), Q value = 0.48
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 187 | 353 | 74 | 19 |
subtype1 | 32 | 85 | 12 | 4 |
subtype2 | 40 | 81 | 31 | 5 |
subtype3 | 115 | 187 | 31 | 10 |
P value = 0.000966 (Chi-square test), Q value = 0.082
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 300 | 221 | 65 | 40 |
subtype1 | 77 | 37 | 11 | 8 |
subtype2 | 66 | 53 | 16 | 20 |
subtype3 | 157 | 131 | 38 | 12 |
P value = 0.000542 (Chi-square test), Q value = 0.048
nPatients | CM0 (I+) | M0 | M1 | MX |
---|---|---|---|---|
ALL | 2 | 523 | 3 | 105 |
subtype1 | 0 | 111 | 0 | 22 |
subtype2 | 0 | 112 | 1 | 44 |
subtype3 | 2 | 300 | 2 | 39 |
P value = 0.358 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 626 | 7 |
subtype1 | 133 | 0 |
subtype2 | 156 | 1 |
subtype3 | 337 | 6 |
P value = 8.86e-34 (Chi-square test), Q value = 1e-31
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 439 | 127 | 5 | 18 | 14 | 29 |
subtype1 | 1 | 111 | 6 | 4 | 0 | 0 | 11 |
subtype2 | 0 | 63 | 86 | 0 | 2 | 4 | 2 |
subtype3 | 0 | 265 | 35 | 1 | 16 | 10 | 16 |
P value = 3.15e-05 (Fisher's exact test), Q value = 0.0032
nPatients | NO | YES |
---|---|---|
ALL | 173 | 460 |
subtype1 | 39 | 94 |
subtype2 | 22 | 135 |
subtype3 | 112 | 231 |
P value = 0.0187 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 562 | 2.5 (5.0) |
subtype1 | 119 | 2.3 (5.3) |
subtype2 | 135 | 3.5 (6.3) |
subtype3 | 308 | 2.1 (4.1) |
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Cluster data file = BRCA-TP.mergedcluster.txt
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Clinical data file = BRCA-TP.merged_data.txt
-
Number of patients = 975
-
Number of clustering approaches = 12
-
Number of selected clinical features = 10
-
Exclude small clusters that include fewer than K patients, K = 3
consensus non-negative matrix factorization clustering approach (Brunet et al. 2004)
Resampling-based clustering method (Monti et al. 2003)
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For continuous numerical clinical features, one-way analysis of variance (Howell 2002) was applied to compare the clinical values between tumor subtypes using 'anova' function in R
For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' 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.