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 1098 patients, 87 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 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', 'NUMBER_OF_LYMPH_NODES', and 'RACE'.
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Consensus hierarchical clustering analysis on array-based mRNA expression data identified 5 subtypes that correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_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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6 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', 'HISTOLOGICAL_TYPE', 'NUMBER_OF_LYMPH_NODES', and 'RACE'.
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CNMF clustering analysis on RPPA data identified 3 subtypes that correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
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Consensus hierarchical clustering analysis on RPPA data identified 6 subtypes that correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', 'NUMBER_OF_LYMPH_NODES', and 'RACE'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that 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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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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4 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to '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 CHIERARCHICAL'. 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 'MIRseq Mature CNMF subtypes'. These subtypes correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_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'.
Table 1. Get Full Table Overview of the association between subtypes identified by 12 different clustering approaches and 12 clinical features. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 87 significant findings detected.
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 |
0.017 (0.032) |
2.82e-08 (1.35e-06) |
0.11 (0.164) |
0.038 (0.0667) |
0.00088 (0.00256) |
0.673 (0.734) |
0.0271 (0.0493) |
0.55 (0.634) |
1e-05 (4.65e-05) |
0.00776 (0.016) |
0.00238 (0.00591) |
0.287 (0.373) |
mRNA cHierClus subtypes |
0.0579 (0.0926) |
4.76e-10 (3.43e-08) |
0.0321 (0.0578) |
0.00559 (0.012) |
0.00429 (0.00965) |
0.63 (0.714) |
0.1 (0.15) |
0.282 (0.369) |
1e-05 (4.65e-05) |
0.0137 (0.0266) |
0.00112 (0.0031) |
0.762 (0.807) |
Copy Number Ratio CNMF subtypes |
0.223 (0.303) |
0.000236 (0.000811) |
0.0432 (0.0735) |
1e-05 (4.65e-05) |
0.00423 (0.00965) |
0.681 (0.734) |
4e-05 (0.000165) |
0.68 (0.734) |
1e-05 (4.65e-05) |
0.00107 (0.00304) |
9e-05 (0.000341) |
0.994 (1.00) |
METHLYATION CNMF |
0.0171 (0.032) |
1.93e-06 (4.65e-05) |
0.00062 (0.00186) |
0.00231 (0.00584) |
0.00129 (0.0035) |
0.359 (0.449) |
0.0737 (0.117) |
0.635 (0.714) |
1e-05 (4.65e-05) |
0.00089 (0.00256) |
1e-05 (4.65e-05) |
0.883 (0.896) |
RPPA CNMF subtypes |
0.311 (0.4) |
0.00197 (0.00507) |
0.0121 (0.0239) |
0.0006 (0.00184) |
0.41 (0.496) |
0.481 (0.577) |
0.0413 (0.0717) |
0.15 (0.218) |
0.00012 (0.000443) |
0.236 (0.318) |
0.055 (0.09) |
1 (1.00) |
RPPA cHierClus subtypes |
0.499 (0.591) |
0.000127 (0.000459) |
0.00521 (0.0114) |
0.00343 (0.00797) |
0.117 (0.172) |
0.373 (0.461) |
0.334 (0.426) |
0.081 (0.125) |
0.00026 (0.000871) |
0.0476 (0.0798) |
0.00273 (0.00655) |
0.683 (0.734) |
RNAseq CNMF subtypes |
0.0992 (0.15) |
1.73e-05 (7.79e-05) |
1e-05 (4.65e-05) |
1e-05 (4.65e-05) |
0.00015 (0.000527) |
0.88 (0.896) |
0.00261 (0.00637) |
0.0807 (0.125) |
1e-05 (4.65e-05) |
0.00328 (0.00774) |
1e-05 (4.65e-05) |
0.188 (0.262) |
RNAseq cHierClus subtypes |
7.89e-06 (4.65e-05) |
1.37e-10 (1.97e-08) |
1e-05 (4.65e-05) |
1e-05 (4.65e-05) |
2e-05 (8.73e-05) |
0.279 (0.369) |
0.0188 (0.0348) |
0.178 (0.251) |
1e-05 (4.65e-05) |
3.58e-05 (0.000152) |
1e-05 (4.65e-05) |
0.549 (0.634) |
MIRSEQ CNMF |
0.352 (0.445) |
0.00663 (0.0138) |
1e-05 (4.65e-05) |
1e-05 (4.65e-05) |
0.0147 (0.0282) |
0.854 (0.884) |
0.163 (0.232) |
0.823 (0.859) |
1e-05 (4.65e-05) |
0.0376 (0.0667) |
1e-05 (4.65e-05) |
0.089 (0.136) |
MIRSEQ CHIERARCHICAL |
0.153 (0.221) |
4.98e-05 (0.000199) |
0.00033 (0.00108) |
0.00143 (0.00381) |
0.00039 (0.00125) |
0.219 (0.301) |
0.0493 (0.0816) |
0.41 (0.496) |
1e-05 (4.65e-05) |
0.00149 (0.0039) |
1e-05 (4.65e-05) |
0.374 (0.461) |
MIRseq Mature CNMF subtypes |
0.884 (0.896) |
0.0434 (0.0735) |
0.00942 (0.0188) |
0.00052 (0.00163) |
0.00473 (0.0105) |
0.199 (0.276) |
0.241 (0.321) |
0.621 (0.71) |
1e-05 (4.65e-05) |
0.0574 (0.0926) |
1e-05 (4.65e-05) |
0.534 (0.625) |
MIRseq Mature cHierClus subtypes |
0.501 (0.591) |
0.00639 (0.0135) |
1e-05 (4.65e-05) |
1e-05 (4.65e-05) |
8e-05 (0.000311) |
0.71 (0.757) |
0.668 (0.734) |
0.776 (0.815) |
1e-05 (4.65e-05) |
0.0084 (0.017) |
1e-05 (4.65e-05) |
0.67 (0.734) |
Table S1. Description of clustering approach #1: 'mRNA CNMF subtypes'
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 |
---|---|---|---|---|---|---|---|---|
Number of samples | 21 | 39 | 121 | 101 | 110 | 74 | 20 | 40 |
P value = 0.017 (logrank test), Q value = 0.032
Table S2. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 512 | 82 | 0.2 - 282.9 (33.1) |
subtype1 | 20 | 3 | 0.3 - 92.0 (15.3) |
subtype2 | 39 | 3 | 1.9 - 157.4 (50.7) |
subtype3 | 116 | 20 | 0.2 - 188.7 (33.1) |
subtype4 | 100 | 14 | 0.2 - 282.9 (33.9) |
subtype5 | 108 | 14 | 0.3 - 281.3 (32.6) |
subtype6 | 71 | 16 | 0.3 - 212.2 (32.8) |
subtype7 | 19 | 4 | 1.0 - 109.0 (49.0) |
subtype8 | 39 | 8 | 0.3 - 112.4 (32.9) |
Figure S1. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #1: 'Time to Death'
![](D1V1.png)
P value = 2.82e-08 (Kruskal-Wallis (anova)), Q value = 1.4e-06
Table S3. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 520 | 58.1 (13.2) |
subtype1 | 20 | 60.7 (13.6) |
subtype2 | 38 | 48.5 (10.6) |
subtype3 | 119 | 58.3 (14.3) |
subtype4 | 101 | 53.8 (12.6) |
subtype5 | 110 | 62.6 (12.5) |
subtype6 | 72 | 59.1 (12.3) |
subtype7 | 20 | 60.4 (9.9) |
subtype8 | 40 | 60.6 (12.0) |
Figure S2. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D1V2.png)
P value = 0.11 (Fisher's exact test), Q value = 0.16
Table S4. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 50 | 36 | 3 | 1 | 183 | 112 | 77 | 15 | 19 | 13 | 1 | 13 |
subtype1 | 1 | 0 | 0 | 0 | 8 | 3 | 5 | 1 | 0 | 2 | 0 | 0 |
subtype2 | 2 | 2 | 0 | 0 | 12 | 10 | 8 | 0 | 2 | 1 | 1 | 1 |
subtype3 | 8 | 7 | 3 | 0 | 35 | 35 | 20 | 6 | 3 | 1 | 0 | 3 |
subtype4 | 9 | 9 | 0 | 0 | 45 | 20 | 9 | 1 | 4 | 2 | 0 | 1 |
subtype5 | 16 | 12 | 0 | 1 | 42 | 15 | 10 | 5 | 2 | 3 | 0 | 4 |
subtype6 | 4 | 2 | 0 | 0 | 21 | 19 | 15 | 2 | 6 | 3 | 0 | 1 |
subtype7 | 4 | 1 | 0 | 0 | 6 | 4 | 4 | 0 | 0 | 0 | 0 | 1 |
subtype8 | 6 | 3 | 0 | 0 | 14 | 6 | 6 | 0 | 2 | 1 | 0 | 2 |
Figure S3. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D1V3.png)
P value = 0.038 (Fisher's exact test), Q value = 0.067
Table S5. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 132 | 312 | 59 | 20 |
subtype1 | 5 | 14 | 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 |
Figure S4. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D1V4.png)
P value = 0.00088 (Fisher's exact test), Q value = 0.0026
Table S6. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 255 | 171 | 60 | 29 |
subtype1 | 6 | 6 | 7 | 1 |
subtype2 | 14 | 16 | 5 | 3 |
subtype3 | 49 | 50 | 14 | 4 |
subtype4 | 64 | 25 | 7 | 5 |
subtype5 | 66 | 31 | 7 | 5 |
subtype6 | 24 | 26 | 14 | 8 |
subtype7 | 11 | 5 | 3 | 0 |
subtype8 | 21 | 12 | 3 | 3 |
Figure S5. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D1V5.png)
P value = 0.673 (Fisher's exact test), Q value = 0.73
Table S7. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 495 | 15 |
subtype1 | 19 | 2 |
subtype2 | 37 | 1 |
subtype3 | 115 | 2 |
subtype4 | 97 | 3 |
subtype5 | 101 | 3 |
subtype6 | 70 | 3 |
subtype7 | 19 | 0 |
subtype8 | 37 | 1 |
Figure S6. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
![](D1V6.png)
P value = 0.0271 (Fisher's exact test), Q value = 0.049
Table S8. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #7: 'GENDER'
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 |
Figure S7. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #7: 'GENDER'
![](D1V7.png)
P value = 0.55 (Fisher's exact test), Q value = 0.63
Table S9. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 203 | 236 |
subtype1 | 7 | 6 |
subtype2 | 15 | 19 |
subtype3 | 55 | 49 |
subtype4 | 36 | 51 |
subtype5 | 45 | 46 |
subtype6 | 27 | 32 |
subtype7 | 6 | 10 |
subtype8 | 12 | 23 |
Figure S8. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D1V8.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S10. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|
ALL | 446 | 43 | 1 | 11 | 2 | 22 |
subtype1 | 20 | 0 | 0 | 0 | 0 | 1 |
subtype2 | 28 | 8 | 0 | 3 | 0 | 0 |
subtype3 | 113 | 1 | 0 | 0 | 1 | 6 |
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 | 22 | 13 | 0 | 3 | 0 | 2 |
Figure S9. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D1V9.png)
P value = 0.00776 (Kruskal-Wallis (anova)), Q value = 0.016
Table S11. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 408 | 1.8 (3.5) |
subtype1 | 14 | 1.4 (2.2) |
subtype2 | 34 | 1.9 (2.4) |
subtype3 | 86 | 1.6 (2.3) |
subtype4 | 93 | 1.4 (3.2) |
subtype5 | 84 | 1.8 (3.9) |
subtype6 | 47 | 2.7 (3.5) |
subtype7 | 15 | 1.2 (2.5) |
subtype8 | 35 | 2.7 (6.3) |
Figure S10. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D1V10.png)
P value = 0.00238 (Fisher's exact test), Q value = 0.0059
Table S12. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 34 | 40 | 361 |
subtype1 | 0 | 2 | 0 | 14 |
subtype2 | 0 | 4 | 3 | 28 |
subtype3 | 0 | 10 | 12 | 74 |
subtype4 | 0 | 6 | 12 | 75 |
subtype5 | 0 | 2 | 5 | 81 |
subtype6 | 1 | 9 | 2 | 43 |
subtype7 | 0 | 1 | 5 | 11 |
subtype8 | 0 | 0 | 1 | 35 |
Figure S11. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #11: 'RACE'
![](D1V11.png)
P value = 0.287 (Fisher's exact test), Q value = 0.37
Table S13. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #12: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 7 | 372 |
subtype1 | 0 | 14 |
subtype2 | 1 | 32 |
subtype3 | 0 | 83 |
subtype4 | 1 | 83 |
subtype5 | 2 | 70 |
subtype6 | 2 | 46 |
subtype7 | 1 | 14 |
subtype8 | 0 | 30 |
Figure S12. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #12: 'ETHNICITY'
![](D1V12.png)
Table S14. Description of clustering approach #2: 'mRNA cHierClus subtypes'
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 102 | 156 | 118 | 92 | 58 |
P value = 0.0579 (logrank test), Q value = 0.093
Table S15. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 512 | 82 | 0.2 - 282.9 (33.1) |
subtype1 | 98 | 17 | 0.2 - 234.3 (33.0) |
subtype2 | 155 | 22 | 0.3 - 281.3 (42.3) |
subtype3 | 113 | 22 | 0.2 - 212.2 (27.1) |
subtype4 | 91 | 13 | 0.3 - 282.9 (35.3) |
subtype5 | 55 | 8 | 0.3 - 206.9 (28.3) |
Figure S13. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'
![](D2V1.png)
P value = 4.76e-10 (Kruskal-Wallis (anova)), Q value = 3.4e-08
Table S16. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 520 | 58.1 (13.2) |
subtype1 | 100 | 59.8 (13.1) |
subtype2 | 154 | 55.2 (13.0) |
subtype3 | 116 | 59.6 (12.2) |
subtype4 | 92 | 53.4 (12.7) |
subtype5 | 58 | 66.9 (11.9) |
Figure S14. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D2V2.png)
P value = 0.0321 (Fisher's exact test), Q value = 0.058
Table S17. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 50 | 36 | 3 | 1 | 183 | 112 | 77 | 15 | 19 | 13 | 1 | 13 |
subtype1 | 6 | 6 | 1 | 0 | 32 | 30 | 16 | 5 | 2 | 1 | 0 | 3 |
subtype2 | 21 | 13 | 2 | 0 | 56 | 24 | 23 | 1 | 6 | 3 | 1 | 5 |
subtype3 | 6 | 4 | 0 | 0 | 36 | 27 | 24 | 5 | 8 | 6 | 0 | 1 |
subtype4 | 9 | 8 | 0 | 0 | 40 | 19 | 8 | 1 | 3 | 2 | 0 | 1 |
subtype5 | 8 | 5 | 0 | 1 | 19 | 12 | 6 | 3 | 0 | 1 | 0 | 3 |
Figure S15. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D2V3.png)
P value = 0.00559 (Fisher's exact test), Q value = 0.012
Table S18. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 132 | 312 | 59 | 20 |
subtype1 | 19 | 63 | 14 | 5 |
subtype2 | 54 | 79 | 19 | 3 |
subtype3 | 18 | 78 | 15 | 7 |
subtype4 | 22 | 60 | 8 | 1 |
subtype5 | 19 | 32 | 3 | 4 |
Figure S16. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D2V4.png)
P value = 0.00429 (Fisher's exact test), Q value = 0.0097
Table S19. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 255 | 171 | 60 | 29 |
subtype1 | 44 | 43 | 9 | 4 |
subtype2 | 81 | 47 | 15 | 9 |
subtype3 | 41 | 39 | 25 | 10 |
subtype4 | 58 | 24 | 6 | 4 |
subtype5 | 31 | 18 | 5 | 2 |
Figure S17. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D2V5.png)
P value = 0.63 (Fisher's exact test), Q value = 0.71
Table S20. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 495 | 15 |
subtype1 | 96 | 2 |
subtype2 | 146 | 3 |
subtype3 | 111 | 6 |
subtype4 | 88 | 3 |
subtype5 | 54 | 1 |
Figure S18. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
![](D2V6.png)
P value = 0.1 (Fisher's exact test), Q value = 0.15
Table S21. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 520 | 6 |
subtype1 | 98 | 4 |
subtype2 | 155 | 1 |
subtype3 | 117 | 1 |
subtype4 | 92 | 0 |
subtype5 | 58 | 0 |
Figure S19. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #7: 'GENDER'
![](D2V7.png)
P value = 0.282 (Fisher's exact test), Q value = 0.37
Table S22. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 203 | 236 |
subtype1 | 44 | 43 |
subtype2 | 63 | 66 |
subtype3 | 47 | 47 |
subtype4 | 30 | 49 |
subtype5 | 19 | 31 |
Figure S20. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D2V8.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S23. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|
ALL | 446 | 43 | 1 | 11 | 2 | 22 |
subtype1 | 97 | 1 | 0 | 0 | 1 | 3 |
subtype2 | 111 | 31 | 0 | 7 | 0 | 7 |
subtype3 | 110 | 6 | 0 | 0 | 0 | 2 |
subtype4 | 84 | 1 | 1 | 0 | 0 | 5 |
subtype5 | 44 | 4 | 0 | 4 | 1 | 5 |
Figure S21. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D2V9.png)
P value = 0.0137 (Kruskal-Wallis (anova)), Q value = 0.027
Table S24. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 408 | 1.8 (3.5) |
subtype1 | 70 | 1.4 (1.9) |
subtype2 | 135 | 2.0 (4.4) |
subtype3 | 74 | 2.4 (3.4) |
subtype4 | 86 | 1.5 (3.3) |
subtype5 | 43 | 1.5 (2.7) |
Figure S22. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D2V10.png)
P value = 0.00112 (Fisher's exact test), Q value = 0.0031
Table S25. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 34 | 40 | 361 |
subtype1 | 0 | 7 | 10 | 60 |
subtype2 | 0 | 6 | 8 | 128 |
subtype3 | 1 | 16 | 4 | 65 |
subtype4 | 0 | 3 | 12 | 70 |
subtype5 | 0 | 2 | 6 | 38 |
Figure S23. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #11: 'RACE'
![](D2V11.png)
P value = 0.762 (Fisher's exact test), Q value = 0.81
Table S26. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #12: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 7 | 372 |
subtype1 | 0 | 66 |
subtype2 | 3 | 119 |
subtype3 | 2 | 74 |
subtype4 | 1 | 75 |
subtype5 | 1 | 38 |
Figure S24. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #12: 'ETHNICITY'
![](D2V12.png)
Table S27. Description of clustering approach #3: 'Copy Number Ratio CNMF subtypes'
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 275 | 407 | 98 | 257 | 43 |
P value = 0.223 (logrank test), Q value = 0.3
Table S28. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 1064 | 147 | 0.0 - 282.9 (27.9) |
subtype1 | 271 | 37 | 0.2 - 162.1 (24.8) |
subtype2 | 399 | 50 | 0.0 - 281.3 (32.5) |
subtype3 | 98 | 14 | 0.3 - 212.2 (24.2) |
subtype4 | 254 | 37 | 0.2 - 282.9 (25.9) |
subtype5 | 42 | 9 | 2.6 - 275.9 (26.0) |
Figure S25. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #1: 'Time to Death'
![](D3V1.png)
P value = 0.000236 (Kruskal-Wallis (anova)), Q value = 0.00081
Table S29. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1065 | 58.6 (13.2) |
subtype1 | 268 | 59.1 (13.9) |
subtype2 | 403 | 58.4 (13.0) |
subtype3 | 97 | 62.1 (12.5) |
subtype4 | 256 | 56.3 (12.8) |
subtype5 | 41 | 63.6 (11.9) |
Figure S26. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D3V2.png)
P value = 0.0432 (Fisher's exact test), Q value = 0.074
Table S30. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
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 | 89 | 85 | 6 | 6 | 353 | 252 | 2 | 154 | 29 | 65 | 20 | 1 | 13 |
subtype1 | 13 | 18 | 2 | 1 | 88 | 66 | 1 | 48 | 13 | 14 | 8 | 0 | 3 |
subtype2 | 48 | 44 | 4 | 3 | 112 | 87 | 1 | 58 | 6 | 29 | 7 | 0 | 7 |
subtype3 | 6 | 4 | 0 | 1 | 32 | 29 | 0 | 9 | 4 | 8 | 2 | 0 | 2 |
subtype4 | 19 | 16 | 0 | 1 | 104 | 59 | 0 | 33 | 6 | 11 | 3 | 1 | 1 |
subtype5 | 3 | 3 | 0 | 0 | 17 | 11 | 0 | 6 | 0 | 3 | 0 | 0 | 0 |
Figure S27. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D3V3.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S31. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
subtype1 | 57 | 177 | 26 | 14 |
subtype2 | 144 | 185 | 68 | 9 |
subtype3 | 12 | 64 | 15 | 7 |
subtype4 | 50 | 173 | 23 | 9 |
subtype5 | 13 | 25 | 4 | 1 |
Figure S28. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D3V4.png)
P value = 0.00423 (Fisher's exact test), Q value = 0.0097
Table S32. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
subtype1 | 104 | 102 | 42 | 18 |
subtype2 | 199 | 133 | 35 | 32 |
subtype3 | 44 | 35 | 6 | 11 |
subtype4 | 143 | 70 | 31 | 13 |
subtype5 | 17 | 18 | 5 | 3 |
Figure S29. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D3V5.png)
P value = 0.681 (Fisher's exact test), Q value = 0.73
Table S33. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 889 | 22 |
subtype1 | 234 | 9 |
subtype2 | 320 | 7 |
subtype3 | 80 | 2 |
subtype4 | 221 | 4 |
subtype5 | 34 | 0 |
Figure S30. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
![](D3V6.png)
P value = 4e-05 (Fisher's exact test), Q value = 0.00016
Table S34. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1068 | 12 |
subtype1 | 264 | 11 |
subtype2 | 407 | 0 |
subtype3 | 97 | 1 |
subtype4 | 257 | 0 |
subtype5 | 43 | 0 |
Figure S31. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #7: 'GENDER'
![](D3V7.png)
P value = 0.68 (Fisher's exact test), Q value = 0.73
Table S35. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 429 | 518 |
subtype1 | 115 | 130 |
subtype2 | 161 | 192 |
subtype3 | 32 | 53 |
subtype4 | 105 | 124 |
subtype5 | 16 | 19 |
Figure S32. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D3V8.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S36. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
subtype1 | 0 | 230 | 26 | 0 | 0 | 6 | 4 | 9 |
subtype2 | 0 | 229 | 123 | 0 | 6 | 14 | 12 | 23 |
subtype3 | 0 | 53 | 37 | 0 | 0 | 5 | 0 | 3 |
subtype4 | 1 | 229 | 6 | 5 | 3 | 4 | 0 | 8 |
subtype5 | 0 | 29 | 8 | 1 | 0 | 0 | 1 | 4 |
Figure S33. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D3V9.png)
P value = 0.00107 (Kruskal-Wallis (anova)), Q value = 0.003
Table S37. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 914 | 2.4 (4.7) |
subtype1 | 210 | 2.6 (4.0) |
subtype2 | 359 | 2.3 (4.7) |
subtype3 | 82 | 3.0 (5.1) |
subtype4 | 224 | 2.0 (4.8) |
subtype5 | 39 | 3.0 (5.9) |
Figure S34. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D3V10.png)
P value = 9e-05 (Fisher's exact test), Q value = 0.00034
Table S38. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
subtype1 | 0 | 22 | 41 | 172 |
subtype2 | 1 | 18 | 54 | 312 |
subtype3 | 0 | 3 | 9 | 74 |
subtype4 | 0 | 15 | 70 | 155 |
subtype5 | 0 | 2 | 7 | 32 |
Figure S35. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #11: 'RACE'
![](D3V11.png)
P value = 0.994 (Fisher's exact test), Q value = 1
Table S39. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #12: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 39 | 875 |
subtype1 | 9 | 214 |
subtype2 | 17 | 339 |
subtype3 | 3 | 73 |
subtype4 | 9 | 213 |
subtype5 | 1 | 36 |
Figure S36. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #12: 'ETHNICITY'
![](D3V12.png)
Table S40. Description of clustering approach #4: 'METHLYATION CNMF'
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 147 | 101 | 216 | 123 | 137 | 59 |
P value = 0.0171 (logrank test), Q value = 0.032
Table S41. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 781 | 102 | 0.0 - 282.9 (27.1) |
subtype1 | 147 | 18 | 0.0 - 162.1 (23.9) |
subtype2 | 101 | 20 | 0.3 - 160.9 (27.1) |
subtype3 | 215 | 21 | 0.2 - 263.3 (25.2) |
subtype4 | 123 | 16 | 1.1 - 216.8 (32.5) |
subtype5 | 136 | 25 | 0.0 - 282.9 (29.9) |
subtype6 | 59 | 2 | 0.3 - 157.4 (28.9) |
Figure S37. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #1: 'Time to Death'
![](D4V1.png)
P value = 1.93e-06 (Kruskal-Wallis (anova)), Q value = 4.6e-05
Table S42. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 770 | 58.2 (13.1) |
subtype1 | 142 | 57.1 (14.7) |
subtype2 | 101 | 63.7 (11.9) |
subtype3 | 213 | 59.8 (13.0) |
subtype4 | 121 | 56.8 (12.1) |
subtype5 | 136 | 55.7 (12.2) |
subtype6 | 57 | 53.8 (12.4) |
Figure S38. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D4V2.png)
P value = 0.00062 (Fisher's exact test), Q value = 0.0019
Table S43. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
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 | 61 | 62 | 5 | 6 | 244 | 187 | 2 | 126 | 19 | 53 | 11 | 5 |
subtype1 | 7 | 6 | 1 | 0 | 44 | 39 | 0 | 28 | 9 | 9 | 2 | 1 |
subtype2 | 7 | 9 | 0 | 2 | 27 | 22 | 1 | 20 | 1 | 9 | 2 | 1 |
subtype3 | 17 | 23 | 2 | 2 | 58 | 56 | 0 | 37 | 5 | 13 | 1 | 2 |
subtype4 | 18 | 9 | 0 | 2 | 43 | 21 | 1 | 18 | 2 | 7 | 2 | 0 |
subtype5 | 6 | 8 | 1 | 0 | 61 | 37 | 0 | 14 | 2 | 3 | 3 | 1 |
subtype6 | 6 | 7 | 1 | 0 | 11 | 12 | 0 | 9 | 0 | 12 | 1 | 0 |
Figure S39. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D4V3.png)
P value = 0.00231 (Fisher's exact test), Q value = 0.0058
Table S44. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 201 | 446 | 109 | 24 |
subtype1 | 26 | 91 | 19 | 10 |
subtype2 | 22 | 58 | 19 | 2 |
subtype3 | 63 | 115 | 32 | 5 |
subtype4 | 46 | 61 | 14 | 2 |
subtype5 | 24 | 92 | 15 | 5 |
subtype6 | 20 | 29 | 10 | 0 |
Figure S40. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D4V4.png)
P value = 0.00129 (Fisher's exact test), Q value = 0.0035
Table S45. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 350 | 269 | 95 | 57 |
subtype1 | 52 | 61 | 21 | 10 |
subtype2 | 47 | 25 | 17 | 9 |
subtype3 | 89 | 85 | 24 | 13 |
subtype4 | 59 | 41 | 15 | 8 |
subtype5 | 81 | 38 | 12 | 5 |
subtype6 | 22 | 19 | 6 | 12 |
Figure S41. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D4V5.png)
P value = 0.359 (Fisher's exact test), Q value = 0.45
Table S46. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 609 | 13 |
subtype1 | 121 | 2 |
subtype2 | 70 | 3 |
subtype3 | 168 | 1 |
subtype4 | 92 | 2 |
subtype5 | 111 | 4 |
subtype6 | 47 | 1 |
Figure S42. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
![](D4V6.png)
P value = 0.0737 (Fisher's exact test), Q value = 0.12
Table S47. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 774 | 9 |
subtype1 | 145 | 2 |
subtype2 | 98 | 3 |
subtype3 | 214 | 2 |
subtype4 | 123 | 0 |
subtype5 | 137 | 0 |
subtype6 | 57 | 2 |
Figure S43. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #7: 'GENDER'
![](D4V7.png)
P value = 0.635 (Fisher's exact test), Q value = 0.71
Table S48. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 309 | 391 |
subtype1 | 61 | 74 |
subtype2 | 38 | 53 |
subtype3 | 90 | 98 |
subtype4 | 49 | 64 |
subtype5 | 54 | 69 |
subtype6 | 17 | 33 |
Figure S44. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D4V8.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S49. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 513 | 178 | 6 | 9 | 25 | 15 | 35 |
subtype1 | 0 | 123 | 11 | 0 | 0 | 5 | 4 | 4 |
subtype2 | 0 | 59 | 35 | 0 | 0 | 4 | 0 | 3 |
subtype3 | 0 | 109 | 70 | 0 | 0 | 11 | 10 | 16 |
subtype4 | 0 | 76 | 38 | 2 | 2 | 3 | 0 | 2 |
subtype5 | 1 | 110 | 4 | 4 | 7 | 1 | 0 | 9 |
subtype6 | 0 | 36 | 20 | 0 | 0 | 1 | 1 | 1 |
Figure S45. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D4V9.png)
P value = 0.00089 (Kruskal-Wallis (anova)), Q value = 0.0026
Table S50. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 718 | 2.6 (4.9) |
subtype1 | 131 | 2.9 (4.9) |
subtype2 | 90 | 3.4 (6.1) |
subtype3 | 203 | 2.4 (4.5) |
subtype4 | 113 | 2.3 (4.8) |
subtype5 | 129 | 1.5 (2.9) |
subtype6 | 52 | 4.7 (6.8) |
Figure S46. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D4V10.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S51. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 38 | 160 | 569 |
subtype1 | 0 | 14 | 34 | 97 |
subtype2 | 0 | 4 | 20 | 74 |
subtype3 | 0 | 5 | 20 | 188 |
subtype4 | 1 | 8 | 25 | 86 |
subtype5 | 0 | 4 | 52 | 78 |
subtype6 | 0 | 3 | 9 | 46 |
Figure S47. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #11: 'RACE'
![](D4V11.png)
P value = 0.883 (Fisher's exact test), Q value = 0.9
Table S52. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #12: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 38 | 676 |
subtype1 | 8 | 127 |
subtype2 | 7 | 88 |
subtype3 | 8 | 185 |
subtype4 | 5 | 107 |
subtype5 | 7 | 117 |
subtype6 | 3 | 52 |
Figure S48. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #12: 'ETHNICITY'
![](D4V12.png)
Table S53. Description of clustering approach #5: 'RPPA CNMF subtypes'
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 156 | 126 | 128 |
P value = 0.311 (logrank test), Q value = 0.4
Table S54. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 398 | 59 | 0.2 - 282.9 (34.0) |
subtype1 | 150 | 27 | 0.2 - 282.9 (32.7) |
subtype2 | 122 | 16 | 0.2 - 263.3 (41.0) |
subtype3 | 126 | 16 | 0.3 - 165.8 (33.1) |
Figure S49. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #1: 'Time to Death'
![](D5V1.png)
P value = 0.00197 (Kruskal-Wallis (anova)), Q value = 0.0051
Table S55. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 408 | 57.9 (13.1) |
subtype1 | 155 | 56.1 (13.2) |
subtype2 | 125 | 56.8 (12.1) |
subtype3 | 128 | 61.1 (13.4) |
Figure S50. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D5V2.png)
P value = 0.0121 (Fisher's exact test), Q value = 0.024
Table S56. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 36 | 29 | 2 | 135 | 97 | 62 | 13 | 15 | 13 | 6 |
subtype1 | 8 | 7 | 0 | 56 | 40 | 23 | 2 | 10 | 7 | 1 |
subtype2 | 16 | 11 | 2 | 34 | 22 | 26 | 6 | 4 | 3 | 2 |
subtype3 | 12 | 11 | 0 | 45 | 35 | 13 | 5 | 1 | 3 | 3 |
Figure S51. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D5V3.png)
P value = 6e-04 (Fisher's exact test), Q value = 0.0018
Table S57. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 94 | 247 | 50 | 18 |
subtype1 | 22 | 108 | 22 | 4 |
subtype2 | 41 | 58 | 18 | 9 |
subtype3 | 31 | 81 | 10 | 5 |
Figure S52. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D5V4.png)
P value = 0.41 (Fisher's exact test), Q value = 0.5
Table S58. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 194 | 133 | 51 | 25 |
subtype1 | 71 | 50 | 20 | 12 |
subtype2 | 58 | 38 | 21 | 7 |
subtype3 | 65 | 45 | 10 | 6 |
Figure S53. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D5V5.png)
P value = 0.481 (Fisher's exact test), Q value = 0.58
Table S59. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 387 | 15 |
subtype1 | 147 | 8 |
subtype2 | 119 | 4 |
subtype3 | 121 | 3 |
Figure S54. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
![](D5V6.png)
P value = 0.0413 (Fisher's exact test), Q value = 0.072
Table S60. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 405 | 5 |
subtype1 | 156 | 0 |
subtype2 | 125 | 1 |
subtype3 | 124 | 4 |
Figure S55. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #7: 'GENDER'
![](D5V7.png)
P value = 0.15 (Fisher's exact test), Q value = 0.22
Table S61. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 161 | 188 |
subtype1 | 59 | 75 |
subtype2 | 43 | 62 |
subtype3 | 59 | 51 |
Figure S56. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D5V8.png)
P value = 0.00012 (Fisher's exact test), Q value = 0.00044
Table S62. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|
ALL | 354 | 31 | 1 | 7 | 2 | 15 |
subtype1 | 143 | 4 | 1 | 1 | 0 | 7 |
subtype2 | 101 | 21 | 0 | 2 | 0 | 2 |
subtype3 | 110 | 6 | 0 | 4 | 2 | 6 |
Figure S57. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D5V9.png)
P value = 0.236 (Kruskal-Wallis (anova)), Q value = 0.32
Table S63. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 334 | 1.8 (3.5) |
subtype1 | 119 | 2.0 (3.5) |
subtype2 | 108 | 2.4 (4.4) |
subtype3 | 107 | 1.1 (2.1) |
Figure S58. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D5V10.png)
P value = 0.055 (Fisher's exact test), Q value = 0.09
Table S64. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 27 | 29 | 295 |
subtype1 | 1 | 17 | 13 | 100 |
subtype2 | 0 | 4 | 8 | 98 |
subtype3 | 0 | 6 | 8 | 97 |
Figure S59. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #11: 'RACE'
![](D5V11.png)
P value = 1 (Fisher's exact test), Q value = 1
Table S65. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #12: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 6 | 298 |
subtype1 | 2 | 116 |
subtype2 | 2 | 89 |
subtype3 | 2 | 93 |
Figure S60. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #12: 'ETHNICITY'
![](D5V12.png)
Table S66. Description of clustering approach #6: 'RPPA cHierClus subtypes'
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 64 | 49 | 93 | 54 | 118 | 32 |
P value = 0.499 (logrank test), Q value = 0.59
Table S67. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 398 | 59 | 0.2 - 282.9 (34.0) |
subtype1 | 63 | 10 | 0.3 - 129.7 (37.2) |
subtype2 | 48 | 6 | 0.3 - 165.8 (32.7) |
subtype3 | 91 | 15 | 0.3 - 282.9 (33.7) |
subtype4 | 54 | 7 | 0.2 - 263.3 (43.0) |
subtype5 | 111 | 16 | 0.2 - 134.1 (32.0) |
subtype6 | 31 | 5 | 0.3 - 102.0 (37.0) |
Figure S61. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'
![](D6V1.png)
P value = 0.000127 (Kruskal-Wallis (anova)), Q value = 0.00046
Table S68. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 408 | 57.9 (13.1) |
subtype1 | 63 | 61.9 (13.8) |
subtype2 | 49 | 61.2 (11.7) |
subtype3 | 93 | 54.1 (13.0) |
subtype4 | 54 | 54.3 (11.1) |
subtype5 | 117 | 59.4 (13.0) |
subtype6 | 32 | 56.5 (13.9) |
Figure S62. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D6V2.png)
P value = 0.00521 (Fisher's exact test), Q value = 0.011
Table S69. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 36 | 29 | 2 | 135 | 97 | 62 | 13 | 15 | 13 | 6 |
subtype1 | 9 | 7 | 0 | 21 | 12 | 5 | 5 | 0 | 2 | 3 |
subtype2 | 7 | 5 | 0 | 17 | 8 | 8 | 2 | 2 | 0 | 0 |
subtype3 | 5 | 5 | 0 | 43 | 21 | 11 | 1 | 3 | 2 | 0 |
subtype4 | 5 | 6 | 2 | 10 | 12 | 12 | 1 | 1 | 3 | 2 |
subtype5 | 9 | 6 | 0 | 34 | 34 | 22 | 4 | 4 | 4 | 1 |
subtype6 | 1 | 0 | 0 | 10 | 10 | 4 | 0 | 5 | 2 | 0 |
Figure S63. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D6V3.png)
P value = 0.00343 (Fisher's exact test), Q value = 0.008
Table S70. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 94 | 247 | 50 | 18 |
subtype1 | 21 | 33 | 3 | 6 |
subtype2 | 16 | 24 | 7 | 2 |
subtype3 | 14 | 68 | 10 | 1 |
subtype4 | 18 | 25 | 7 | 4 |
subtype5 | 20 | 77 | 18 | 3 |
subtype6 | 5 | 20 | 5 | 2 |
Figure S64. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D6V4.png)
P value = 0.117 (Fisher's exact test), Q value = 0.17
Table S71. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 194 | 133 | 51 | 25 |
subtype1 | 35 | 19 | 5 | 3 |
subtype2 | 26 | 14 | 6 | 2 |
subtype3 | 53 | 26 | 10 | 4 |
subtype4 | 21 | 18 | 11 | 3 |
subtype5 | 51 | 42 | 16 | 7 |
subtype6 | 8 | 14 | 3 | 6 |
Figure S65. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D6V5.png)
P value = 0.373 (Fisher's exact test), Q value = 0.46
Table S72. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 387 | 15 |
subtype1 | 58 | 2 |
subtype2 | 49 | 0 |
subtype3 | 89 | 3 |
subtype4 | 47 | 4 |
subtype5 | 114 | 4 |
subtype6 | 30 | 2 |
Figure S66. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
![](D6V6.png)
P value = 0.334 (Fisher's exact test), Q value = 0.43
Table S73. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 405 | 5 |
subtype1 | 63 | 1 |
subtype2 | 49 | 0 |
subtype3 | 93 | 0 |
subtype4 | 54 | 0 |
subtype5 | 114 | 4 |
subtype6 | 32 | 0 |
Figure S67. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #7: 'GENDER'
![](D6V7.png)
P value = 0.081 (Fisher's exact test), Q value = 0.13
Table S74. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 161 | 188 |
subtype1 | 26 | 30 |
subtype2 | 14 | 25 |
subtype3 | 33 | 50 |
subtype4 | 17 | 28 |
subtype5 | 56 | 41 |
subtype6 | 15 | 14 |
Figure S68. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D6V8.png)
P value = 0.00026 (Fisher's exact test), Q value = 0.00087
Table S75. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|
ALL | 354 | 31 | 1 | 7 | 2 | 15 |
subtype1 | 59 | 1 | 0 | 3 | 0 | 1 |
subtype2 | 39 | 9 | 0 | 1 | 0 | 0 |
subtype3 | 86 | 0 | 1 | 0 | 0 | 6 |
subtype4 | 43 | 8 | 0 | 2 | 0 | 1 |
subtype5 | 98 | 11 | 0 | 1 | 2 | 6 |
subtype6 | 29 | 2 | 0 | 0 | 0 | 1 |
Figure S69. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D6V9.png)
P value = 0.0476 (Kruskal-Wallis (anova)), Q value = 0.08
Table S76. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 334 | 1.8 (3.5) |
subtype1 | 49 | 0.9 (1.9) |
subtype2 | 46 | 2.1 (4.4) |
subtype3 | 82 | 1.8 (3.6) |
subtype4 | 45 | 2.6 (4.6) |
subtype5 | 90 | 1.6 (2.6) |
subtype6 | 22 | 3.1 (4.2) |
Figure S70. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D6V10.png)
P value = 0.00273 (Fisher's exact test), Q value = 0.0066
Table S77. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 27 | 29 | 295 |
subtype1 | 0 | 3 | 4 | 46 |
subtype2 | 0 | 1 | 1 | 44 |
subtype3 | 0 | 7 | 13 | 65 |
subtype4 | 0 | 0 | 3 | 44 |
subtype5 | 0 | 10 | 7 | 79 |
subtype6 | 1 | 6 | 1 | 17 |
Figure S71. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #11: 'RACE'
![](D6V11.png)
P value = 0.683 (Fisher's exact test), Q value = 0.73
Table S78. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #12: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 6 | 298 |
subtype1 | 1 | 47 |
subtype2 | 0 | 36 |
subtype3 | 1 | 77 |
subtype4 | 2 | 36 |
subtype5 | 2 | 78 |
subtype6 | 0 | 24 |
Figure S72. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #12: 'ETHNICITY'
![](D6V12.png)
Table S79. Description of clustering approach #7: 'RNAseq CNMF subtypes'
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 567 | 311 | 215 |
P value = 0.0992 (logrank test), Q value = 0.15
Table S80. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 1077 | 150 | 0.0 - 282.9 (28.0) |
subtype1 | 556 | 76 | 0.2 - 281.3 (25.4) |
subtype2 | 307 | 51 | 0.0 - 282.9 (26.9) |
subtype3 | 214 | 23 | 0.3 - 216.8 (34.1) |
Figure S73. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #1: 'Time to Death'
![](D7V1.png)
P value = 1.73e-05 (Kruskal-Wallis (anova)), Q value = 7.8e-05
Table S81. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1078 | 58.6 (13.2) |
subtype1 | 556 | 60.3 (13.5) |
subtype2 | 308 | 57.0 (12.8) |
subtype3 | 214 | 56.5 (12.3) |
Figure S74. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D7V2.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S82. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
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 | 89 | 87 | 6 | 6 | 359 | 255 | 2 | 155 | 29 | 65 | 20 | 1 | 14 |
subtype1 | 46 | 44 | 5 | 2 | 178 | 129 | 1 | 93 | 22 | 24 | 12 | 0 | 10 |
subtype2 | 19 | 22 | 0 | 2 | 132 | 73 | 0 | 33 | 6 | 14 | 5 | 0 | 1 |
subtype3 | 24 | 21 | 1 | 2 | 49 | 53 | 1 | 29 | 1 | 27 | 3 | 1 | 3 |
Figure S75. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D7V3.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S83. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 280 | 632 | 137 | 40 |
subtype1 | 148 | 326 | 64 | 27 |
subtype2 | 65 | 206 | 28 | 11 |
subtype3 | 67 | 100 | 45 | 2 |
Figure S76. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D7V4.png)
P value = 0.00015 (Fisher's exact test), Q value = 0.00053
Table S84. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 515 | 361 | 120 | 77 |
subtype1 | 253 | 194 | 76 | 31 |
subtype2 | 168 | 95 | 28 | 16 |
subtype3 | 94 | 72 | 16 | 30 |
Figure S77. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D7V5.png)
P value = 0.88 (Fisher's exact test), Q value = 0.9
Table S85. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 902 | 22 |
subtype1 | 473 | 13 |
subtype2 | 266 | 6 |
subtype3 | 163 | 3 |
Figure S78. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
![](D7V6.png)
P value = 0.00261 (Fisher's exact test), Q value = 0.0064
Table S86. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1081 | 12 |
subtype1 | 555 | 12 |
subtype2 | 311 | 0 |
subtype3 | 215 | 0 |
Figure S79. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #7: 'GENDER'
![](D7V7.png)
P value = 0.0807 (Fisher's exact test), Q value = 0.13
Table S87. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 435 | 523 |
subtype1 | 233 | 263 |
subtype2 | 129 | 142 |
subtype3 | 73 | 118 |
Figure S80. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D7V8.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S88. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 783 | 202 | 6 | 9 | 28 | 17 | 46 |
subtype1 | 0 | 414 | 90 | 0 | 0 | 17 | 17 | 29 |
subtype2 | 1 | 271 | 8 | 6 | 9 | 3 | 0 | 12 |
subtype3 | 0 | 98 | 104 | 0 | 0 | 8 | 0 | 5 |
Figure S81. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D7V9.png)
P value = 0.00328 (Kruskal-Wallis (anova)), Q value = 0.0077
Table S89. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 925 | 2.4 (4.6) |
subtype1 | 460 | 2.1 (3.8) |
subtype2 | 265 | 1.9 (4.3) |
subtype3 | 200 | 3.5 (6.3) |
Figure S82. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D7V10.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S90. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 61 | 183 | 753 |
subtype1 | 0 | 33 | 71 | 396 |
subtype2 | 1 | 23 | 89 | 178 |
subtype3 | 0 | 5 | 23 | 179 |
Figure S83. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #11: 'RACE'
![](D7V11.png)
P value = 0.188 (Fisher's exact test), Q value = 0.26
Table S91. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #12: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 39 | 880 |
subtype1 | 25 | 439 |
subtype2 | 7 | 261 |
subtype3 | 7 | 180 |
Figure S84. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #12: 'ETHNICITY'
![](D7V12.png)
Table S92. Description of clustering approach #8: 'RNAseq cHierClus subtypes'
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 294 | 166 | 91 | 294 | 188 | 60 |
P value = 7.89e-06 (logrank test), Q value = 4.6e-05
Table S93. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 1077 | 150 | 0.0 - 282.9 (28.0) |
subtype1 | 287 | 41 | 0.2 - 275.9 (25.1) |
subtype2 | 163 | 35 | 0.0 - 212.2 (23.1) |
subtype3 | 91 | 9 | 0.3 - 157.4 (37.2) |
subtype4 | 292 | 26 | 0.3 - 281.3 (32.2) |
subtype5 | 186 | 27 | 0.2 - 282.9 (28.4) |
subtype6 | 58 | 12 | 0.0 - 100.7 (20.2) |
Figure S85. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'
![](D8V1.png)
P value = 1.37e-10 (Kruskal-Wallis (anova)), Q value = 2e-08
Table S94. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
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) |
Figure S86. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D8V2.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S95. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
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 | 89 | 87 | 6 | 6 | 359 | 255 | 2 | 155 | 29 | 65 | 20 | 1 | 14 |
subtype1 | 20 | 23 | 4 | 2 | 95 | 74 | 1 | 43 | 15 | 7 | 4 | 0 | 6 |
subtype2 | 7 | 8 | 0 | 1 | 51 | 38 | 0 | 31 | 8 | 12 | 7 | 0 | 2 |
subtype3 | 7 | 10 | 1 | 1 | 17 | 27 | 0 | 14 | 1 | 12 | 1 | 0 | 0 |
subtype4 | 41 | 26 | 1 | 1 | 87 | 62 | 0 | 43 | 0 | 23 | 3 | 1 | 5 |
subtype5 | 13 | 15 | 0 | 1 | 86 | 41 | 0 | 17 | 4 | 5 | 3 | 0 | 1 |
subtype6 | 1 | 5 | 0 | 0 | 23 | 13 | 1 | 7 | 1 | 6 | 2 | 0 | 0 |
Figure S87. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D8V3.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S96. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 280 | 632 | 137 | 40 |
subtype1 | 76 | 170 | 28 | 18 |
subtype2 | 25 | 110 | 21 | 10 |
subtype3 | 26 | 37 | 27 | 1 |
subtype4 | 95 | 156 | 40 | 2 |
subtype5 | 40 | 124 | 17 | 6 |
subtype6 | 18 | 35 | 4 | 3 |
Figure S88. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D8V4.png)
P value = 2e-05 (Fisher's exact test), Q value = 8.7e-05
Table S97. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
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 |
Figure S89. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D8V5.png)
P value = 0.279 (Fisher's exact test), Q value = 0.37
Table S98. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 902 | 22 |
subtype1 | 250 | 5 |
subtype2 | 134 | 7 |
subtype3 | 69 | 1 |
subtype4 | 235 | 3 |
subtype5 | 162 | 4 |
subtype6 | 52 | 2 |
Figure S90. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
![](D8V6.png)
P value = 0.0188 (Fisher's exact test), Q value = 0.035
Table S99. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1081 | 12 |
subtype1 | 285 | 9 |
subtype2 | 164 | 2 |
subtype3 | 91 | 0 |
subtype4 | 293 | 1 |
subtype5 | 188 | 0 |
subtype6 | 60 | 0 |
Figure S91. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #7: 'GENDER'
![](D8V7.png)
P value = 0.178 (Fisher's exact test), Q value = 0.25
Table S100. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 435 | 523 |
subtype1 | 127 | 136 |
subtype2 | 68 | 70 |
subtype3 | 41 | 39 |
subtype4 | 103 | 156 |
subtype5 | 70 | 97 |
subtype6 | 26 | 25 |
Figure S92. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D8V8.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S101. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 783 | 202 | 6 | 9 | 28 | 17 | 46 |
subtype1 | 0 | 224 | 24 | 0 | 0 | 10 | 15 | 21 |
subtype2 | 0 | 138 | 16 | 0 | 3 | 4 | 1 | 4 |
subtype3 | 0 | 28 | 55 | 0 | 0 | 5 | 1 | 2 |
subtype4 | 0 | 176 | 100 | 1 | 0 | 7 | 0 | 10 |
subtype5 | 1 | 163 | 2 | 5 | 5 | 2 | 0 | 9 |
subtype6 | 0 | 54 | 5 | 0 | 1 | 0 | 0 | 0 |
Figure S93. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D8V9.png)
P value = 3.58e-05 (Kruskal-Wallis (anova)), Q value = 0.00015
Table S102. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
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) |
Figure S94. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D8V10.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S103. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #11: 'RACE'
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 |
Figure S95. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #11: 'RACE'
![](D8V11.png)
P value = 0.549 (Fisher's exact test), Q value = 0.63
Table S104. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #12: 'ETHNICITY'
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 |
Figure S96. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #12: 'ETHNICITY'
![](D8V12.png)
Table S105. Description of clustering approach #9: 'MIRSEQ CNMF'
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 309 | 214 | 274 | 281 |
P value = 0.352 (logrank test), Q value = 0.44
Table S106. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 1062 | 146 | 0.0 - 282.9 (27.7) |
subtype1 | 304 | 47 | 0.0 - 255.7 (25.0) |
subtype2 | 214 | 28 | 0.0 - 282.9 (32.6) |
subtype3 | 269 | 32 | 0.2 - 281.3 (26.0) |
subtype4 | 275 | 39 | 0.3 - 275.9 (29.1) |
Figure S97. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #1: 'Time to Death'
![](D9V1.png)
P value = 0.00663 (Kruskal-Wallis (anova)), Q value = 0.014
Table S107. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1063 | 58.6 (13.2) |
subtype1 | 308 | 57.8 (13.1) |
subtype2 | 211 | 57.2 (12.8) |
subtype3 | 270 | 60.7 (13.4) |
subtype4 | 274 | 58.5 (13.3) |
Figure S98. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D9V2.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S108. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
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 | 89 | 87 | 7 | 6 | 354 | 249 | 2 | 152 | 28 | 64 | 20 | 1 | 14 |
subtype1 | 14 | 17 | 0 | 2 | 132 | 69 | 0 | 40 | 7 | 13 | 8 | 0 | 3 |
subtype2 | 24 | 21 | 2 | 2 | 45 | 58 | 1 | 31 | 3 | 23 | 3 | 1 | 0 |
subtype3 | 16 | 27 | 4 | 1 | 89 | 57 | 1 | 37 | 11 | 20 | 3 | 0 | 8 |
subtype4 | 35 | 22 | 1 | 1 | 88 | 65 | 0 | 44 | 7 | 8 | 6 | 0 | 3 |
Figure S99. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D9V3.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S109. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 281 | 619 | 134 | 40 |
subtype1 | 49 | 215 | 32 | 11 |
subtype2 | 72 | 95 | 43 | 3 |
subtype3 | 67 | 155 | 36 | 15 |
subtype4 | 93 | 154 | 23 | 11 |
Figure S100. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D9V4.png)
P value = 0.0147 (Fisher's exact test), Q value = 0.028
Table S110. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 509 | 356 | 118 | 75 |
subtype1 | 165 | 90 | 33 | 16 |
subtype2 | 89 | 83 | 17 | 24 |
subtype3 | 128 | 86 | 30 | 22 |
subtype4 | 127 | 97 | 38 | 13 |
Figure S101. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D9V5.png)
P value = 0.854 (Fisher's exact test), Q value = 0.88
Table S111. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 887 | 21 |
subtype1 | 259 | 8 |
subtype2 | 160 | 3 |
subtype3 | 220 | 4 |
subtype4 | 248 | 6 |
Figure S102. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
![](D9V6.png)
P value = 0.163 (Fisher's exact test), Q value = 0.23
Table S112. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1066 | 12 |
subtype1 | 303 | 6 |
subtype2 | 214 | 0 |
subtype3 | 272 | 2 |
subtype4 | 277 | 4 |
Figure S103. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #7: 'GENDER'
![](D9V7.png)
P value = 0.823 (Fisher's exact test), Q value = 0.86
Table S113. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 431 | 513 |
subtype1 | 127 | 144 |
subtype2 | 86 | 104 |
subtype3 | 106 | 139 |
subtype4 | 112 | 126 |
Figure S104. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D9V8.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S114. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 199 | 6 | 9 | 28 | 17 | 47 |
subtype1 | 1 | 269 | 9 | 5 | 5 | 4 | 5 | 10 |
subtype2 | 0 | 89 | 106 | 0 | 4 | 3 | 3 | 9 |
subtype3 | 0 | 177 | 66 | 0 | 0 | 10 | 8 | 13 |
subtype4 | 0 | 235 | 18 | 1 | 0 | 11 | 1 | 15 |
Figure S105. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D9V9.png)
P value = 0.0376 (Kruskal-Wallis (anova)), Q value = 0.067
Table S115. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 916 | 2.4 (4.6) |
subtype1 | 258 | 2.0 (4.2) |
subtype2 | 201 | 3.2 (6.0) |
subtype3 | 220 | 2.5 (5.0) |
subtype4 | 237 | 1.9 (3.1) |
Figure S106. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D9V10.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S116. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 61 | 182 | 746 |
subtype1 | 0 | 20 | 91 | 176 |
subtype2 | 0 | 11 | 30 | 169 |
subtype3 | 0 | 9 | 43 | 189 |
subtype4 | 1 | 21 | 18 | 212 |
Figure S107. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #11: 'RACE'
![](D9V11.png)
P value = 0.089 (Fisher's exact test), Q value = 0.14
Table S117. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #12: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 39 | 874 |
subtype1 | 5 | 261 |
subtype2 | 11 | 187 |
subtype3 | 10 | 212 |
subtype4 | 13 | 214 |
Figure S108. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #12: 'ETHNICITY'
![](D9V12.png)
Table S118. Description of clustering approach #10: 'MIRSEQ CHIERARCHICAL'
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 300 | 155 | 248 | 141 | 98 | 136 |
P value = 0.153 (logrank test), Q value = 0.22
Table S119. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 1062 | 146 | 0.0 - 282.9 (27.7) |
subtype1 | 294 | 46 | 0.0 - 263.3 (26.3) |
subtype2 | 152 | 24 | 0.0 - 216.8 (21.8) |
subtype3 | 248 | 29 | 0.3 - 170.2 (25.5) |
subtype4 | 140 | 17 | 0.3 - 281.3 (36.4) |
subtype5 | 94 | 10 | 0.2 - 275.9 (26.6) |
subtype6 | 134 | 20 | 0.2 - 282.9 (31.0) |
Figure S109. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #1: 'Time to Death'
![](D10V1.png)
P value = 4.98e-05 (Kruskal-Wallis (anova)), Q value = 2e-04
Table S120. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1063 | 58.6 (13.2) |
subtype1 | 295 | 58.3 (13.6) |
subtype2 | 151 | 58.8 (12.8) |
subtype3 | 243 | 59.5 (13.0) |
subtype4 | 141 | 58.2 (12.0) |
subtype5 | 97 | 63.4 (14.7) |
subtype6 | 136 | 54.5 (12.1) |
Figure S110. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D10V2.png)
P value = 0.00033 (Fisher's exact test), Q value = 0.0011
Table S121. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
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 | 89 | 87 | 7 | 6 | 354 | 249 | 2 | 152 | 28 | 64 | 20 | 1 | 14 |
subtype1 | 18 | 23 | 2 | 2 | 96 | 67 | 1 | 48 | 8 | 17 | 7 | 1 | 8 |
subtype2 | 12 | 9 | 1 | 2 | 56 | 33 | 0 | 23 | 3 | 9 | 6 | 0 | 0 |
subtype3 | 16 | 29 | 2 | 1 | 62 | 67 | 1 | 40 | 3 | 24 | 1 | 0 | 2 |
subtype4 | 26 | 8 | 1 | 0 | 44 | 32 | 0 | 11 | 6 | 9 | 3 | 0 | 1 |
subtype5 | 9 | 6 | 1 | 0 | 32 | 23 | 0 | 18 | 6 | 1 | 1 | 0 | 1 |
subtype6 | 8 | 12 | 0 | 1 | 64 | 27 | 0 | 12 | 2 | 4 | 2 | 0 | 2 |
Figure S111. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D10V3.png)
P value = 0.00143 (Fisher's exact test), Q value = 0.0038
Table S122. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 281 | 619 | 134 | 40 |
subtype1 | 70 | 182 | 34 | 12 |
subtype2 | 40 | 95 | 15 | 5 |
subtype3 | 66 | 128 | 49 | 4 |
subtype4 | 51 | 69 | 13 | 8 |
subtype5 | 26 | 53 | 12 | 7 |
subtype6 | 28 | 92 | 11 | 4 |
Figure S112. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D10V4.png)
P value = 0.00039 (Fisher's exact test), Q value = 0.0012
Table S123. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 509 | 356 | 118 | 75 |
subtype1 | 121 | 106 | 40 | 22 |
subtype2 | 74 | 44 | 23 | 11 |
subtype3 | 111 | 85 | 23 | 26 |
subtype4 | 73 | 47 | 10 | 11 |
subtype5 | 43 | 40 | 12 | 1 |
subtype6 | 87 | 34 | 10 | 4 |
Figure S113. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D10V5.png)
P value = 0.219 (Fisher's exact test), Q value = 0.3
Table S124. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 887 | 21 |
subtype1 | 251 | 8 |
subtype2 | 126 | 6 |
subtype3 | 186 | 1 |
subtype4 | 123 | 3 |
subtype5 | 85 | 1 |
subtype6 | 116 | 2 |
Figure S114. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
![](D10V6.png)
P value = 0.0493 (Fisher's exact test), Q value = 0.082
Table S125. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1066 | 12 |
subtype1 | 296 | 4 |
subtype2 | 152 | 3 |
subtype3 | 248 | 0 |
subtype4 | 139 | 2 |
subtype5 | 95 | 3 |
subtype6 | 136 | 0 |
Figure S115. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #7: 'GENDER'
![](D10V7.png)
P value = 0.41 (Fisher's exact test), Q value = 0.5
Table S126. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 431 | 513 |
subtype1 | 112 | 152 |
subtype2 | 60 | 75 |
subtype3 | 106 | 125 |
subtype4 | 60 | 51 |
subtype5 | 41 | 42 |
subtype6 | 52 | 68 |
Figure S116. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D10V8.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S127. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 199 | 6 | 9 | 28 | 17 | 47 |
subtype1 | 0 | 252 | 22 | 1 | 0 | 10 | 1 | 14 |
subtype2 | 0 | 131 | 11 | 0 | 6 | 1 | 0 | 6 |
subtype3 | 0 | 100 | 134 | 0 | 1 | 3 | 3 | 7 |
subtype4 | 0 | 99 | 28 | 0 | 0 | 9 | 0 | 5 |
subtype5 | 0 | 70 | 2 | 0 | 0 | 3 | 13 | 10 |
subtype6 | 1 | 118 | 2 | 5 | 2 | 2 | 0 | 5 |
Figure S117. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D10V9.png)
P value = 0.00149 (Kruskal-Wallis (anova)), Q value = 0.0039
Table S128. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 916 | 2.4 (4.6) |
subtype1 | 233 | 2.4 (4.1) |
subtype2 | 131 | 2.7 (5.3) |
subtype3 | 225 | 3.1 (5.8) |
subtype4 | 130 | 2.2 (4.6) |
subtype5 | 76 | 1.8 (3.1) |
subtype6 | 121 | 1.2 (2.5) |
Figure S118. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D10V10.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S129. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 61 | 182 | 746 |
subtype1 | 1 | 22 | 44 | 197 |
subtype2 | 0 | 13 | 27 | 102 |
subtype3 | 0 | 12 | 39 | 194 |
subtype4 | 0 | 5 | 8 | 119 |
subtype5 | 0 | 4 | 10 | 64 |
subtype6 | 0 | 5 | 54 | 70 |
Figure S119. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #11: 'RACE'
![](D10V11.png)
P value = 0.374 (Fisher's exact test), Q value = 0.46
Table S130. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #12: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 39 | 874 |
subtype1 | 7 | 230 |
subtype2 | 6 | 127 |
subtype3 | 10 | 224 |
subtype4 | 8 | 110 |
subtype5 | 5 | 65 |
subtype6 | 3 | 118 |
Figure S120. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #12: 'ETHNICITY'
![](D10V12.png)
Table S131. Description of clustering approach #11: 'MIRseq Mature CNMF subtypes'
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 182 | 140 | 102 | 111 | 133 |
P value = 0.884 (logrank test), Q value = 0.9
Table S132. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 663 | 86 | 0.0 - 216.8 (26.0) |
subtype1 | 181 | 29 | 0.5 - 212.2 (26.1) |
subtype2 | 138 | 18 | 0.0 - 131.7 (29.9) |
subtype3 | 101 | 7 | 0.2 - 109.3 (23.5) |
subtype4 | 111 | 15 | 0.3 - 120.6 (30.4) |
subtype5 | 132 | 17 | 0.0 - 216.8 (25.5) |
Figure S121. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #1: 'Time to Death'
![](D11V1.png)
P value = 0.0434 (Kruskal-Wallis (anova)), Q value = 0.074
Table S133. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 653 | 58.3 (13.2) |
subtype1 | 174 | 58.4 (14.1) |
subtype2 | 140 | 57.0 (12.9) |
subtype3 | 100 | 61.1 (12.7) |
subtype4 | 110 | 56.3 (12.6) |
subtype5 | 129 | 59.1 (12.9) |
Figure S122. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D11V2.png)
P value = 0.00942 (Fisher's exact test), Q value = 0.019
Table S134. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
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 | 52 | 5 | 5 | 219 | 162 | 2 | 92 | 13 | 42 | 8 | 2 |
subtype1 | 20 | 17 | 1 | 1 | 63 | 41 | 0 | 26 | 4 | 6 | 1 | 1 |
subtype2 | 10 | 7 | 0 | 1 | 65 | 28 | 0 | 20 | 3 | 3 | 1 | 0 |
subtype3 | 5 | 12 | 3 | 2 | 25 | 24 | 0 | 14 | 1 | 13 | 3 | 0 |
subtype4 | 15 | 8 | 1 | 0 | 31 | 30 | 0 | 14 | 2 | 7 | 1 | 1 |
subtype5 | 12 | 8 | 0 | 1 | 35 | 39 | 2 | 18 | 3 | 13 | 2 | 0 |
Figure S123. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D11V3.png)
P value = 0.00052 (Fisher's exact test), Q value = 0.0016
Table S135. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 185 | 378 | 85 | 19 |
subtype1 | 60 | 101 | 14 | 6 |
subtype2 | 28 | 97 | 10 | 5 |
subtype3 | 23 | 56 | 21 | 2 |
subtype4 | 42 | 53 | 14 | 2 |
subtype5 | 32 | 71 | 26 | 4 |
Figure S124. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D11V4.png)
P value = 0.00473 (Fisher's exact test), Q value = 0.01
Table S136. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 318 | 229 | 67 | 45 |
subtype1 | 85 | 67 | 19 | 7 |
subtype2 | 82 | 36 | 19 | 3 |
subtype3 | 45 | 34 | 7 | 13 |
subtype4 | 48 | 45 | 10 | 7 |
subtype5 | 58 | 47 | 12 | 15 |
Figure S125. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D11V5.png)
P value = 0.199 (Fisher's exact test), Q value = 0.28
Table S137. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 515 | 8 |
subtype1 | 158 | 1 |
subtype2 | 112 | 1 |
subtype3 | 56 | 3 |
subtype4 | 84 | 1 |
subtype5 | 105 | 2 |
Figure S126. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
![](D11V6.png)
P value = 0.241 (Fisher's exact test), Q value = 0.32
Table S138. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 659 | 9 |
subtype1 | 178 | 4 |
subtype2 | 139 | 1 |
subtype3 | 99 | 3 |
subtype4 | 110 | 1 |
subtype5 | 133 | 0 |
Figure S127. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #7: 'GENDER'
![](D11V7.png)
P value = 0.621 (Fisher's exact test), Q value = 0.71
Table S139. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 275 | 327 |
subtype1 | 82 | 80 |
subtype2 | 53 | 74 |
subtype3 | 41 | 54 |
subtype4 | 40 | 49 |
subtype5 | 59 | 70 |
Figure S128. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D11V8.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S140. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 437 | 160 | 5 | 9 | 15 | 15 | 26 |
subtype1 | 0 | 146 | 13 | 0 | 0 | 8 | 6 | 9 |
subtype2 | 1 | 123 | 3 | 5 | 4 | 2 | 0 | 2 |
subtype3 | 0 | 41 | 52 | 0 | 0 | 2 | 4 | 3 |
subtype4 | 0 | 63 | 34 | 0 | 3 | 2 | 1 | 8 |
subtype5 | 0 | 64 | 58 | 0 | 2 | 1 | 4 | 4 |
Figure S129. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D11V9.png)
P value = 0.0574 (Kruskal-Wallis (anova)), Q value = 0.093
Table S141. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 600 | 2.5 (5.0) |
subtype1 | 159 | 2.0 (4.0) |
subtype2 | 131 | 1.5 (2.7) |
subtype3 | 87 | 3.4 (6.1) |
subtype4 | 104 | 2.6 (4.9) |
subtype5 | 119 | 3.4 (7.0) |
Figure S130. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D11V10.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S142. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #11: 'RACE'
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 51 | 145 | 466 |
subtype1 | 20 | 11 | 151 |
subtype2 | 10 | 54 | 74 |
subtype3 | 1 | 39 | 60 |
subtype4 | 4 | 14 | 92 |
subtype5 | 16 | 27 | 89 |
Figure S131. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #11: 'RACE'
![](D11V11.png)
P value = 0.534 (Fisher's exact test), Q value = 0.62
Table S143. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #12: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 29 | 608 |
subtype1 | 8 | 167 |
subtype2 | 3 | 130 |
subtype3 | 4 | 90 |
subtype4 | 7 | 97 |
subtype5 | 7 | 124 |
Figure S132. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #12: 'ETHNICITY'
![](D11V12.png)
Table S144. Description of clustering approach #12: 'MIRseq Mature cHierClus subtypes'
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 309 | 249 | 110 |
P value = 0.501 (logrank test), Q value = 0.59
Table S145. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 663 | 86 | 0.0 - 216.8 (26.0) |
subtype1 | 304 | 46 | 0.2 - 160.9 (29.2) |
subtype2 | 249 | 25 | 0.0 - 216.8 (22.3) |
subtype3 | 110 | 15 | 1.5 - 212.2 (33.4) |
Figure S133. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'
![](D12V1.png)
P value = 0.00639 (Kruskal-Wallis (anova)), Q value = 0.014
Table S146. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 653 | 58.3 (13.2) |
subtype1 | 301 | 57.6 (13.7) |
subtype2 | 243 | 60.2 (12.7) |
subtype3 | 109 | 55.8 (12.3) |
Figure S134. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D12V2.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S147. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
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 | 52 | 5 | 5 | 219 | 162 | 2 | 92 | 13 | 42 | 8 | 2 |
subtype1 | 27 | 22 | 1 | 3 | 124 | 68 | 0 | 44 | 7 | 7 | 3 | 1 |
subtype2 | 16 | 20 | 4 | 2 | 62 | 67 | 2 | 37 | 5 | 31 | 3 | 0 |
subtype3 | 19 | 10 | 0 | 0 | 33 | 27 | 0 | 11 | 1 | 4 | 2 | 1 |
Figure S135. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D12V3.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S148. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 185 | 378 | 85 | 19 |
subtype1 | 78 | 193 | 26 | 11 |
subtype2 | 61 | 130 | 53 | 5 |
subtype3 | 46 | 55 | 6 | 3 |
Figure S136. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D12V4.png)
P value = 8e-05 (Fisher's exact test), Q value = 0.00031
Table S149. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 318 | 229 | 67 | 45 |
subtype1 | 160 | 99 | 37 | 8 |
subtype2 | 107 | 85 | 22 | 32 |
subtype3 | 51 | 45 | 8 | 5 |
Figure S137. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D12V5.png)
P value = 0.71 (Fisher's exact test), Q value = 0.76
Table S150. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 515 | 8 |
subtype1 | 258 | 3 |
subtype2 | 167 | 3 |
subtype3 | 90 | 2 |
Figure S138. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
![](D12V6.png)
P value = 0.668 (Fisher's exact test), Q value = 0.73
Table S151. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 659 | 9 |
subtype1 | 304 | 5 |
subtype2 | 247 | 2 |
subtype3 | 108 | 2 |
Figure S139. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #7: 'GENDER'
![](D12V7.png)
P value = 0.776 (Fisher's exact test), Q value = 0.82
Table S152. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 275 | 327 |
subtype1 | 131 | 146 |
subtype2 | 104 | 131 |
subtype3 | 40 | 50 |
Figure S140. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D12V8.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S153. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 437 | 160 | 5 | 9 | 15 | 15 | 26 |
subtype1 | 1 | 253 | 16 | 5 | 2 | 9 | 9 | 14 |
subtype2 | 0 | 103 | 126 | 0 | 7 | 2 | 5 | 6 |
subtype3 | 0 | 81 | 18 | 0 | 0 | 4 | 1 | 6 |
Figure S141. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D12V9.png)
P value = 0.0084 (Kruskal-Wallis (anova)), Q value = 0.017
Table S154. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 600 | 2.5 (5.0) |
subtype1 | 275 | 1.8 (3.7) |
subtype2 | 221 | 3.6 (6.5) |
subtype3 | 104 | 2.1 (4.2) |
Figure S142. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D12V10.png)
P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05
Table S155. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #11: 'RACE'
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 51 | 145 | 466 |
subtype1 | 27 | 67 | 213 |
subtype2 | 18 | 72 | 156 |
subtype3 | 6 | 6 | 97 |
Figure S143. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #11: 'RACE'
![](D12V11.png)
P value = 0.67 (Fisher's exact test), Q value = 0.73
Table S156. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #12: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 29 | 608 |
subtype1 | 14 | 280 |
subtype2 | 9 | 230 |
subtype3 | 6 | 98 |
Figure S144. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #12: 'ETHNICITY'
![](D12V12.png)
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Cluster data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BRCA-TP/20125499/BRCA-TP.mergedcluster.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BRCA-TP/19775058/BRCA-TP.merged_data.txt
-
Number of patients = 1098
-
Number of clustering approaches = 12
-
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.