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 14 clinical features across 625 patients, 59 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 4 subtypes that correlate to 'TUMOR_TISSUE_SITE', 'PATHOLOGIC_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', 'RESIDUAL_TUMOR', and 'NUMBER_OF_LYMPH_NODES'.
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Consensus hierarchical clustering analysis on array-based mRNA expression data identified 4 subtypes that correlate to 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'PATHOLOGIC_STAGE', 'RADIATION_THERAPY', 'HISTOLOGICAL_TYPE', and 'RESIDUAL_TUMOR'.
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3 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes correlate to 'TUMOR_TISSUE_SITE', 'PATHOLOGIC_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', 'RESIDUAL_TUMOR', and 'NUMBER_OF_LYMPH_NODES'.
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3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.
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CNMF clustering analysis on RPPA data identified 7 subtypes that correlate to 'PATHOLOGIC_STAGE', 'RESIDUAL_TUMOR', 'RACE', and 'ETHNICITY'.
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Consensus hierarchical clustering analysis on RPPA data identified 3 subtypes that correlate to 'PATHOLOGIC_STAGE' and 'RESIDUAL_TUMOR'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', 'RESIDUAL_TUMOR', and 'NUMBER_OF_LYMPH_NODES'.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 7 subtypes that correlate to 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'PATHOLOGIC_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'RESIDUAL_TUMOR', and 'NUMBER_OF_LYMPH_NODES'.
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3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'PATHOLOGIC_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'RESIDUAL_TUMOR', and 'NUMBER_OF_LYMPH_NODES'.
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3 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', and 'RESIDUAL_TUMOR'.
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6 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes correlate to 'TUMOR_TISSUE_SITE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.
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4 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes correlate to 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
Table 1. Get Full Table Overview of the association between subtypes identified by 12 different clustering approaches and 14 clinical features. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 59 significant findings detected.
Clinical Features |
Statistical Tests |
mRNA CNMF subtypes |
mRNA cHierClus subtypes |
Copy Number Ratio CNMF subtypes |
METHLYATION CNMF |
RPPA CNMF subtypes |
RPPA cHierClus subtypes |
RNAseq CNMF subtypes |
RNAseq cHierClus subtypes |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRseq Mature CNMF subtypes |
MIRseq Mature cHierClus subtypes |
Time to Death | logrank test |
0.312 (0.506) |
0.223 (0.4) |
0.646 (0.811) |
0.75 (0.881) |
0.63 (0.808) |
0.817 (0.909) |
0.0987 (0.234) |
0.445 (0.651) |
0.0609 (0.162) |
0.846 (0.923) |
0.855 (0.923) |
0.503 (0.716) |
YEARS TO BIRTH | Kruskal-Wallis (anova) |
0.434 (0.651) |
0.0483 (0.141) |
0.512 (0.722) |
0.000195 (0.00156) |
0.621 (0.807) |
0.125 (0.282) |
0.00283 (0.0168) |
0.00104 (0.00728) |
0.00875 (0.0397) |
0.00428 (0.0211) |
0.201 (0.375) |
0.516 (0.722) |
TUMOR TISSUE SITE | Fisher's exact test |
0.0253 (0.087) |
0.0029 (0.0168) |
1e-05 (0.000129) |
0.00135 (0.00907) |
0.624 (0.807) |
0.169 (0.342) |
0.0959 (0.233) |
1e-05 (0.000129) |
0.0396 (0.123) |
0.261 (0.438) |
1e-05 (0.000129) |
1e-05 (0.000129) |
PATHOLOGIC STAGE | Fisher's exact test |
0.0056 (0.0269) |
0.0492 (0.141) |
0.00323 (0.0181) |
0.658 (0.815) |
0.0119 (0.0502) |
0.00408 (0.0208) |
0.00386 (0.0203) |
3e-05 (0.000315) |
0.00028 (0.00214) |
0.012 (0.0502) |
0.194 (0.366) |
0.767 (0.894) |
PATHOLOGY T STAGE | Fisher's exact test |
0.0573 (0.158) |
0.0614 (0.162) |
0.555 (0.752) |
0.804 (0.907) |
0.913 (0.964) |
0.605 (0.798) |
0.0414 (0.126) |
0.68 (0.822) |
0.0969 (0.233) |
0.903 (0.96) |
0.143 (0.307) |
0.441 (0.651) |
PATHOLOGY N STAGE | Fisher's exact test |
0.0163 (0.0623) |
0.46 (0.666) |
0.00014 (0.00124) |
0.175 (0.346) |
0.283 (0.466) |
0.595 (0.793) |
0.112 (0.258) |
0.0149 (0.0594) |
0.0152 (0.0594) |
0.147 (0.313) |
0.214 (0.396) |
0.749 (0.881) |
PATHOLOGY M STAGE | Fisher's exact test |
0.0265 (0.0876) |
0.0846 (0.209) |
0.00378 (0.0203) |
0.644 (0.811) |
0.128 (0.282) |
0.445 (0.651) |
0.0843 (0.209) |
0.101 (0.235) |
0.817 (0.909) |
0.192 (0.366) |
0.0254 (0.087) |
0.473 (0.679) |
GENDER | Fisher's exact test |
0.0615 (0.162) |
0.187 (0.361) |
0.225 (0.4) |
0.16 (0.331) |
0.354 (0.552) |
0.647 (0.811) |
0.608 (0.798) |
0.361 (0.552) |
0.543 (0.742) |
0.52 (0.722) |
0.857 (0.923) |
0.323 (0.517) |
RADIATION THERAPY | Fisher's exact test |
0.98 (1.00) |
0.018 (0.0657) |
0.313 (0.506) |
0.159 (0.331) |
0.778 (0.901) |
0.18 (0.352) |
0.0673 (0.174) |
0.726 (0.865) |
0.71 (0.852) |
0.84 (0.923) |
0.361 (0.552) |
0.00861 (0.0397) |
HISTOLOGICAL TYPE | Fisher's exact test |
1e-05 (0.000129) |
1e-05 (0.000129) |
1e-05 (0.000129) |
1e-05 (0.000129) |
0.226 (0.4) |
0.274 (0.456) |
2e-05 (0.000224) |
1e-05 (0.000129) |
5e-05 (0.000494) |
0.237 (0.411) |
1e-05 (0.000129) |
1e-05 (0.000129) |
RESIDUAL TUMOR | Fisher's exact test |
0.0178 (0.0657) |
0.00991 (0.0438) |
0.0266 (0.0876) |
0.242 (0.414) |
0.00079 (0.00577) |
0.00015 (0.00126) |
2e-05 (0.000224) |
1e-05 (0.000129) |
1e-05 (0.000129) |
0.00013 (0.00121) |
0.534 (0.735) |
0.357 (0.552) |
NUMBER OF LYMPH NODES | Kruskal-Wallis (anova) |
0.0127 (0.0521) |
0.174 (0.346) |
0.0028 (0.0168) |
0.948 (0.99) |
0.246 (0.417) |
0.679 (0.822) |
0.0494 (0.141) |
0.0207 (0.074) |
0.0488 (0.141) |
0.127 (0.282) |
0.0318 (0.103) |
0.348 (0.552) |
RACE | Fisher's exact test |
0.134 (0.293) |
0.168 (0.342) |
0.671 (0.822) |
0.431 (0.651) |
0.00284 (0.0168) |
0.787 (0.902) |
0.863 (0.923) |
0.0561 (0.157) |
0.659 (0.815) |
0.791 (0.902) |
0.218 (0.398) |
0.795 (0.902) |
ETHNICITY | Fisher's exact test |
1 (1.00) |
0.86 (0.923) |
0.0335 (0.106) |
0.077 (0.196) |
0.237 (0.411) |
0.937 (0.984) |
1 (1.00) |
0.594 (0.793) |
Table S1. Description of clustering approach #1: 'mRNA CNMF subtypes'
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 46 | 62 | 72 | 42 |
P value = 0.312 (logrank test), Q value = 0.51
Table S2. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 211 | 40 | 0.0 - 54.0 (21.0) |
subtype1 | 42 | 9 | 0.0 - 46.6 (23.0) |
subtype2 | 58 | 15 | 1.0 - 52.0 (20.5) |
subtype3 | 69 | 10 | 0.0 - 50.0 (20.1) |
subtype4 | 42 | 6 | 0.0 - 54.0 (22.0) |
Figure S1. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #1: 'Time to Death'

P value = 0.434 (Kruskal-Wallis (anova)), Q value = 0.65
Table S3. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 222 | 69.5 (11.4) |
subtype1 | 46 | 70.8 (11.8) |
subtype2 | 62 | 68.5 (8.9) |
subtype3 | 72 | 69.5 (12.4) |
subtype4 | 42 | 69.6 (12.6) |
Figure S2. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

P value = 0.0253 (Fisher's exact test), Q value = 0.087
Table S4. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'
nPatients | COLON | RECTUM |
---|---|---|
ALL | 152 | 68 |
subtype1 | 39 | 7 |
subtype2 | 37 | 25 |
subtype3 | 45 | 25 |
subtype4 | 31 | 11 |
Figure S3. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

P value = 0.0056 (Fisher's exact test), Q value = 0.027
Table S5. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 47 | 15 | 65 | 5 | 10 | 3 | 22 | 20 | 33 | 1 |
subtype1 | 8 | 3 | 15 | 3 | 3 | 1 | 4 | 2 | 6 | 0 |
subtype2 | 9 | 2 | 14 | 0 | 2 | 2 | 5 | 11 | 17 | 0 |
subtype3 | 19 | 4 | 23 | 0 | 4 | 0 | 7 | 7 | 8 | 0 |
subtype4 | 11 | 6 | 13 | 2 | 1 | 0 | 6 | 0 | 2 | 1 |
Figure S4. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

P value = 0.0573 (Fisher's exact test), Q value = 0.16
Table S6. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 9 | 46 | 148 | 19 |
subtype1 | 1 | 9 | 30 | 6 |
subtype2 | 1 | 12 | 41 | 8 |
subtype3 | 5 | 16 | 51 | 0 |
subtype4 | 2 | 9 | 26 | 5 |
Figure S5. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

P value = 0.0163 (Fisher's exact test), Q value = 0.062
Table S7. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 136 | 43 | 43 |
subtype1 | 30 | 6 | 10 |
subtype2 | 28 | 17 | 17 |
subtype3 | 46 | 12 | 14 |
subtype4 | 32 | 8 | 2 |
Figure S6. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

P value = 0.0265 (Fisher's exact test), Q value = 0.088
Table S8. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 186 | 34 |
subtype1 | 39 | 6 |
subtype2 | 45 | 17 |
subtype3 | 63 | 8 |
subtype4 | 39 | 3 |
Figure S7. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

P value = 0.0615 (Fisher's exact test), Q value = 0.16
Table S9. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #8: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 106 | 116 |
subtype1 | 28 | 18 |
subtype2 | 33 | 29 |
subtype3 | 30 | 42 |
subtype4 | 15 | 27 |
Figure S8. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #8: 'GENDER'

P value = 0.98 (Fisher's exact test), Q value = 1
Table S10. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #9: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 165 | 13 |
subtype1 | 33 | 2 |
subtype2 | 45 | 3 |
subtype3 | 54 | 5 |
subtype4 | 33 | 3 |
Figure S9. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #9: 'RADIATION_THERAPY'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013
Table S11. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 129 | 22 | 58 | 7 |
subtype1 | 28 | 11 | 4 | 2 |
subtype2 | 36 | 1 | 25 | 0 |
subtype3 | 44 | 1 | 21 | 2 |
subtype4 | 21 | 9 | 8 | 3 |
Figure S10. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

P value = 0.0178 (Fisher's exact test), Q value = 0.066
Table S12. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #11: 'RESIDUAL_TUMOR'
nPatients | R0 | R1 | R2 |
---|---|---|---|
ALL | 185 | 2 | 29 |
subtype1 | 38 | 0 | 4 |
subtype2 | 45 | 2 | 15 |
subtype3 | 62 | 0 | 8 |
subtype4 | 40 | 0 | 2 |
Figure S11. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

P value = 0.0127 (Kruskal-Wallis (anova)), Q value = 0.052
Table S13. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 221 | 2.2 (4.7) |
subtype1 | 46 | 3.3 (7.0) |
subtype2 | 62 | 2.9 (5.4) |
subtype3 | 72 | 1.6 (2.7) |
subtype4 | 41 | 0.8 (2.2) |
Figure S12. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

P value = 0.134 (Fisher's exact test), Q value = 0.29
Table S14. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #13: 'RACE'
nPatients | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|
ALL | 2 | 15 |
subtype1 | 0 | 7 |
subtype2 | 2 | 3 |
subtype3 | 0 | 4 |
subtype4 | 0 | 1 |
Figure S13. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #13: 'RACE'

Table S15. Description of clustering approach #2: 'mRNA cHierClus subtypes'
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 52 | 41 | 77 | 52 |
P value = 0.223 (logrank test), Q value = 0.4
Table S16. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 211 | 40 | 0.0 - 54.0 (21.0) |
subtype1 | 49 | 11 | 0.0 - 53.0 (22.0) |
subtype2 | 39 | 11 | 1.0 - 48.0 (24.0) |
subtype3 | 76 | 13 | 0.0 - 54.0 (19.5) |
subtype4 | 47 | 5 | 0.9 - 50.0 (22.0) |
Figure S14. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'

P value = 0.0483 (Kruskal-Wallis (anova)), Q value = 0.14
Table S17. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 222 | 69.5 (11.4) |
subtype1 | 52 | 72.9 (11.6) |
subtype2 | 41 | 67.7 (9.6) |
subtype3 | 77 | 68.1 (11.7) |
subtype4 | 52 | 69.5 (11.6) |
Figure S15. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

P value = 0.0029 (Fisher's exact test), Q value = 0.017
Table S18. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'
nPatients | COLON | RECTUM |
---|---|---|
ALL | 152 | 68 |
subtype1 | 46 | 6 |
subtype2 | 24 | 17 |
subtype3 | 48 | 28 |
subtype4 | 34 | 17 |
Figure S16. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

P value = 0.0492 (Fisher's exact test), Q value = 0.14
Table S19. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 47 | 15 | 65 | 5 | 10 | 3 | 22 | 20 | 33 | 1 |
subtype1 | 9 | 3 | 17 | 4 | 3 | 1 | 6 | 2 | 5 | 1 |
subtype2 | 4 | 2 | 10 | 1 | 0 | 1 | 4 | 7 | 12 | 0 |
subtype3 | 20 | 8 | 23 | 0 | 6 | 1 | 5 | 5 | 9 | 0 |
subtype4 | 14 | 2 | 15 | 0 | 1 | 0 | 7 | 6 | 7 | 0 |
Figure S17. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

P value = 0.0614 (Fisher's exact test), Q value = 0.16
Table S20. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 9 | 46 | 148 | 19 |
subtype1 | 1 | 10 | 33 | 8 |
subtype2 | 0 | 7 | 28 | 6 |
subtype3 | 7 | 15 | 51 | 4 |
subtype4 | 1 | 14 | 36 | 1 |
Figure S18. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

P value = 0.46 (Fisher's exact test), Q value = 0.67
Table S21. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 136 | 43 | 43 |
subtype1 | 34 | 9 | 9 |
subtype2 | 19 | 11 | 11 |
subtype3 | 52 | 12 | 13 |
subtype4 | 31 | 11 | 10 |
Figure S19. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

P value = 0.0846 (Fisher's exact test), Q value = 0.21
Table S22. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 186 | 34 |
subtype1 | 45 | 6 |
subtype2 | 29 | 12 |
subtype3 | 68 | 9 |
subtype4 | 44 | 7 |
Figure S20. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

P value = 0.187 (Fisher's exact test), Q value = 0.36
Table S23. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #8: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 106 | 116 |
subtype1 | 30 | 22 |
subtype2 | 22 | 19 |
subtype3 | 34 | 43 |
subtype4 | 20 | 32 |
Figure S21. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #8: 'GENDER'

P value = 0.018 (Fisher's exact test), Q value = 0.066
Table S24. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #9: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 165 | 13 |
subtype1 | 37 | 2 |
subtype2 | 30 | 1 |
subtype3 | 57 | 10 |
subtype4 | 41 | 0 |
Figure S22. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #9: 'RADIATION_THERAPY'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013
Table S25. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 129 | 22 | 58 | 7 |
subtype1 | 27 | 18 | 2 | 3 |
subtype2 | 24 | 0 | 17 | 0 |
subtype3 | 44 | 4 | 23 | 3 |
subtype4 | 34 | 0 | 16 | 1 |
Figure S23. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

P value = 0.00991 (Fisher's exact test), Q value = 0.044
Table S26. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #11: 'RESIDUAL_TUMOR'
nPatients | R0 | R1 | R2 |
---|---|---|---|
ALL | 185 | 2 | 29 |
subtype1 | 45 | 0 | 3 |
subtype2 | 28 | 2 | 11 |
subtype3 | 69 | 0 | 8 |
subtype4 | 43 | 0 | 7 |
Figure S24. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

P value = 0.174 (Kruskal-Wallis (anova)), Q value = 0.35
Table S27. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 221 | 2.2 (4.7) |
subtype1 | 52 | 2.8 (6.4) |
subtype2 | 41 | 3.3 (6.4) |
subtype3 | 76 | 1.5 (2.9) |
subtype4 | 52 | 1.6 (2.6) |
Figure S25. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

P value = 0.168 (Fisher's exact test), Q value = 0.34
Table S28. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #13: 'RACE'
nPatients | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|
ALL | 2 | 15 |
subtype1 | 0 | 6 |
subtype2 | 2 | 3 |
subtype3 | 0 | 5 |
subtype4 | 0 | 1 |
Figure S26. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #13: 'RACE'

Table S29. Description of clustering approach #3: 'Copy Number Ratio CNMF subtypes'
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 253 | 207 | 152 |
P value = 0.646 (logrank test), Q value = 0.81
Table S30. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 593 | 121 | 0.0 - 148.0 (20.0) |
subtype1 | 243 | 55 | 0.0 - 148.0 (20.0) |
subtype2 | 201 | 35 | 0.1 - 131.5 (20.0) |
subtype3 | 149 | 31 | 0.0 - 130.7 (21.4) |
Figure S27. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #1: 'Time to Death'

P value = 0.512 (Kruskal-Wallis (anova)), Q value = 0.72
Table S31. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 610 | 66.3 (12.8) |
subtype1 | 251 | 66.7 (14.1) |
subtype2 | 207 | 66.2 (11.2) |
subtype3 | 152 | 65.7 (12.4) |
Figure S28. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013
Table S32. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'
nPatients | COLON | RECTUM |
---|---|---|
ALL | 446 | 162 |
subtype1 | 210 | 43 |
subtype2 | 132 | 71 |
subtype3 | 104 | 48 |
Figure S29. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

P value = 0.00323 (Fisher's exact test), Q value = 0.018
Table S33. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 104 | 1 | 36 | 173 | 10 | 3 | 26 | 18 | 83 | 54 | 63 | 26 | 2 |
subtype1 | 53 | 1 | 18 | 82 | 6 | 0 | 12 | 5 | 28 | 19 | 16 | 6 | 1 |
subtype2 | 33 | 0 | 5 | 56 | 3 | 1 | 9 | 7 | 34 | 14 | 26 | 13 | 1 |
subtype3 | 18 | 0 | 13 | 35 | 1 | 2 | 5 | 6 | 21 | 21 | 21 | 7 | 0 |
Figure S30. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

P value = 0.555 (Fisher's exact test), Q value = 0.75
Table S34. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 20 | 106 | 417 | 67 |
subtype1 | 10 | 50 | 163 | 29 |
subtype2 | 8 | 32 | 144 | 22 |
subtype3 | 2 | 24 | 110 | 16 |
Figure S31. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

P value = 0.00014 (Fisher's exact test), Q value = 0.0012
Table S35. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 345 | 150 | 115 |
subtype1 | 166 | 48 | 39 |
subtype2 | 105 | 67 | 34 |
subtype3 | 74 | 35 | 42 |
Figure S32. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

P value = 0.00378 (Fisher's exact test), Q value = 0.02
Table S36. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 450 | 88 |
subtype1 | 197 | 22 |
subtype2 | 146 | 39 |
subtype3 | 107 | 27 |
Figure S33. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

P value = 0.225 (Fisher's exact test), Q value = 0.4
Table S37. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #8: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 287 | 325 |
subtype1 | 128 | 125 |
subtype2 | 88 | 119 |
subtype3 | 71 | 81 |
Figure S34. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #8: 'GENDER'

P value = 0.313 (Fisher's exact test), Q value = 0.51
Table S38. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #9: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 446 | 28 |
subtype1 | 187 | 8 |
subtype2 | 153 | 13 |
subtype3 | 106 | 7 |
Figure S35. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #9: 'RADIATION_THERAPY'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013
Table S39. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 382 | 60 | 146 | 13 |
subtype1 | 159 | 48 | 33 | 9 |
subtype2 | 127 | 5 | 71 | 0 |
subtype3 | 96 | 7 | 42 | 4 |
Figure S36. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

P value = 0.0266 (Fisher's exact test), Q value = 0.088
Table S40. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #11: 'RESIDUAL_TUMOR'
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 442 | 5 | 37 | 29 |
subtype1 | 185 | 3 | 9 | 17 |
subtype2 | 155 | 0 | 13 | 6 |
subtype3 | 102 | 2 | 15 | 6 |
Figure S37. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

P value = 0.0028 (Kruskal-Wallis (anova)), Q value = 0.017
Table S41. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 576 | 2.2 (4.7) |
subtype1 | 237 | 1.8 (4.3) |
subtype2 | 195 | 1.9 (3.4) |
subtype3 | 144 | 3.3 (6.5) |
Figure S38. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

P value = 0.671 (Fisher's exact test), Q value = 0.82
Table S42. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #13: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 12 | 64 | 292 |
subtype1 | 1 | 7 | 26 | 127 |
subtype2 | 0 | 2 | 25 | 93 |
subtype3 | 0 | 3 | 13 | 72 |
Figure S39. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #13: 'RACE'

P value = 1 (Fisher's exact test), Q value = 1
Table S43. Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #14: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 5 | 348 |
subtype1 | 2 | 153 |
subtype2 | 2 | 113 |
subtype3 | 1 | 82 |
Figure S40. Get High-res Image Clustering Approach #3: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #14: 'ETHNICITY'

Table S44. Description of clustering approach #4: 'METHLYATION CNMF'
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 101 | 159 | 130 |
P value = 0.75 (logrank test), Q value = 0.88
Table S45. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 384 | 80 | 0.1 - 148.0 (19.8) |
subtype1 | 99 | 20 | 0.7 - 148.0 (19.1) |
subtype2 | 157 | 30 | 0.1 - 139.2 (21.0) |
subtype3 | 128 | 30 | 0.1 - 140.4 (19.5) |
Figure S41. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #1: 'Time to Death'

P value = 0.000195 (Kruskal-Wallis (anova)), Q value = 0.0016
Table S46. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 388 | 64.4 (13.0) |
subtype1 | 100 | 60.4 (13.6) |
subtype2 | 159 | 64.3 (12.1) |
subtype3 | 129 | 67.7 (12.8) |
Figure S42. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

P value = 0.00135 (Fisher's exact test), Q value = 0.0091
Table S47. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'
nPatients | COLON | RECTUM |
---|---|---|
ALL | 292 | 96 |
subtype1 | 71 | 28 |
subtype2 | 109 | 50 |
subtype3 | 112 | 18 |
Figure S43. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

P value = 0.658 (Fisher's exact test), Q value = 0.81
Table S48. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 54 | 1 | 20 | 114 | 7 | 3 | 11 | 15 | 61 | 35 | 29 | 25 | 2 |
subtype1 | 13 | 0 | 5 | 30 | 1 | 0 | 2 | 5 | 13 | 11 | 8 | 8 | 0 |
subtype2 | 18 | 0 | 9 | 44 | 2 | 2 | 4 | 9 | 31 | 11 | 12 | 12 | 1 |
subtype3 | 23 | 1 | 6 | 40 | 4 | 1 | 5 | 1 | 17 | 13 | 9 | 5 | 1 |
Figure S44. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

P value = 0.804 (Fisher's exact test), Q value = 0.91
Table S49. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 11 | 56 | 271 | 50 |
subtype1 | 3 | 11 | 71 | 15 |
subtype2 | 5 | 22 | 114 | 18 |
subtype3 | 3 | 23 | 86 | 17 |
Figure S45. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

P value = 0.175 (Fisher's exact test), Q value = 0.35
Table S50. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 213 | 103 | 71 |
subtype1 | 53 | 28 | 19 |
subtype2 | 82 | 50 | 25 |
subtype3 | 78 | 25 | 27 |
Figure S46. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

P value = 0.644 (Fisher's exact test), Q value = 0.81
Table S51. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 264 | 53 |
subtype1 | 69 | 14 |
subtype2 | 108 | 25 |
subtype3 | 87 | 14 |
Figure S47. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

P value = 0.16 (Fisher's exact test), Q value = 0.33
Table S52. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #8: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 178 | 212 |
subtype1 | 41 | 60 |
subtype2 | 69 | 90 |
subtype3 | 68 | 62 |
Figure S48. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #8: 'GENDER'

P value = 0.159 (Fisher's exact test), Q value = 0.33
Table S53. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #9: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 286 | 15 |
subtype1 | 79 | 4 |
subtype2 | 108 | 9 |
subtype3 | 99 | 2 |
Figure S49. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #9: 'RADIATION_THERAPY'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013
Table S54. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 251 | 38 | 90 | 6 |
subtype1 | 55 | 16 | 27 | 1 |
subtype2 | 104 | 3 | 48 | 2 |
subtype3 | 92 | 19 | 15 | 3 |
Figure S50. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

P value = 0.242 (Fisher's exact test), Q value = 0.41
Table S55. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #11: 'RESIDUAL_TUMOR'
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 256 | 4 | 7 | 29 |
subtype1 | 68 | 1 | 1 | 5 |
subtype2 | 110 | 1 | 2 | 9 |
subtype3 | 78 | 2 | 4 | 15 |
Figure S51. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

P value = 0.948 (Kruskal-Wallis (anova)), Q value = 0.99
Table S56. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 354 | 2.3 (4.8) |
subtype1 | 92 | 2.5 (5.0) |
subtype2 | 145 | 2.1 (5.1) |
subtype3 | 117 | 2.3 (4.2) |
Figure S52. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

P value = 0.431 (Fisher's exact test), Q value = 0.65
Table S57. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #13: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 12 | 62 | 282 |
subtype1 | 1 | 3 | 15 | 78 |
subtype2 | 0 | 3 | 23 | 118 |
subtype3 | 0 | 6 | 24 | 86 |
Figure S53. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #13: 'RACE'

P value = 0.86 (Fisher's exact test), Q value = 0.92
Table S58. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #14: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 5 | 335 |
subtype1 | 1 | 91 |
subtype2 | 3 | 136 |
subtype3 | 1 | 108 |
Figure S54. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #14: 'ETHNICITY'

Table S59. Description of clustering approach #5: 'RPPA CNMF subtypes'
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
---|---|---|---|---|---|---|---|
Number of samples | 77 | 87 | 46 | 65 | 108 | 92 | 13 |
P value = 0.63 (logrank test), Q value = 0.81
Table S60. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 474 | 98 | 0.0 - 140.4 (20.0) |
subtype1 | 73 | 16 | 0.1 - 129.3 (17.8) |
subtype2 | 86 | 22 | 0.5 - 140.4 (23.7) |
subtype3 | 44 | 7 | 0.0 - 131.5 (21.0) |
subtype4 | 62 | 17 | 0.7 - 124.3 (17.8) |
subtype5 | 107 | 18 | 0.7 - 135.7 (20.0) |
subtype6 | 89 | 17 | 0.0 - 88.2 (20.0) |
subtype7 | 13 | 1 | 1.0 - 83.0 (19.0) |
Figure S55. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #1: 'Time to Death'

P value = 0.621 (Kruskal-Wallis (anova)), Q value = 0.81
Table S61. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 487 | 66.6 (12.7) |
subtype1 | 77 | 66.3 (12.1) |
subtype2 | 87 | 66.3 (11.4) |
subtype3 | 45 | 67.3 (14.0) |
subtype4 | 65 | 66.3 (14.0) |
subtype5 | 108 | 65.1 (12.8) |
subtype6 | 92 | 68.0 (13.0) |
subtype7 | 13 | 71.1 (9.0) |
Figure S56. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

P value = 0.624 (Fisher's exact test), Q value = 0.81
Table S62. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'
nPatients | COLON | RECTUM |
---|---|---|
ALL | 357 | 131 |
subtype1 | 59 | 18 |
subtype2 | 66 | 21 |
subtype3 | 30 | 16 |
subtype4 | 51 | 14 |
subtype5 | 79 | 29 |
subtype6 | 63 | 29 |
subtype7 | 9 | 4 |
Figure S57. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

P value = 0.0119 (Fisher's exact test), Q value = 0.05
Table S63. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 1 | 27 | 148 | 9 | 2 | 24 | 15 | 69 | 42 | 46 | 20 | 2 |
subtype1 | 10 | 0 | 0 | 25 | 0 | 0 | 1 | 3 | 15 | 9 | 8 | 6 | 0 |
subtype2 | 11 | 1 | 4 | 25 | 1 | 1 | 7 | 3 | 10 | 4 | 11 | 6 | 0 |
subtype3 | 10 | 0 | 0 | 11 | 0 | 0 | 4 | 0 | 7 | 6 | 5 | 1 | 0 |
subtype4 | 9 | 0 | 5 | 16 | 2 | 0 | 3 | 3 | 14 | 5 | 5 | 1 | 1 |
subtype5 | 16 | 0 | 5 | 41 | 4 | 1 | 3 | 4 | 14 | 12 | 2 | 5 | 1 |
subtype6 | 17 | 0 | 13 | 25 | 2 | 0 | 5 | 1 | 9 | 6 | 12 | 1 | 0 |
subtype7 | 2 | 0 | 0 | 5 | 0 | 0 | 1 | 1 | 0 | 0 | 3 | 0 | 0 |
Figure S58. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

P value = 0.913 (Fisher's exact test), Q value = 0.96
Table S64. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 11 | 81 | 339 | 55 |
subtype1 | 0 | 11 | 55 | 11 |
subtype2 | 2 | 13 | 61 | 10 |
subtype3 | 2 | 8 | 31 | 4 |
subtype4 | 1 | 12 | 44 | 8 |
subtype5 | 4 | 15 | 74 | 15 |
subtype6 | 2 | 19 | 64 | 7 |
subtype7 | 0 | 3 | 10 | 0 |
Figure S59. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

P value = 0.283 (Fisher's exact test), Q value = 0.47
Table S65. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 274 | 122 | 89 |
subtype1 | 37 | 20 | 20 |
subtype2 | 47 | 27 | 13 |
subtype3 | 22 | 10 | 13 |
subtype4 | 34 | 19 | 12 |
subtype5 | 68 | 24 | 16 |
subtype6 | 59 | 18 | 14 |
subtype7 | 7 | 4 | 1 |
Figure S60. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

P value = 0.128 (Fisher's exact test), Q value = 0.28
Table S66. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 367 | 67 |
subtype1 | 54 | 14 |
subtype2 | 57 | 16 |
subtype3 | 35 | 6 |
subtype4 | 49 | 7 |
subtype5 | 89 | 8 |
subtype6 | 75 | 13 |
subtype7 | 8 | 3 |
Figure S61. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

P value = 0.354 (Fisher's exact test), Q value = 0.55
Table S67. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #8: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 233 | 255 |
subtype1 | 37 | 40 |
subtype2 | 37 | 50 |
subtype3 | 29 | 17 |
subtype4 | 34 | 31 |
subtype5 | 47 | 61 |
subtype6 | 43 | 49 |
subtype7 | 6 | 7 |
Figure S62. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #8: 'GENDER'

P value = 0.778 (Fisher's exact test), Q value = 0.9
Table S68. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #9: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 357 | 23 |
subtype1 | 52 | 2 |
subtype2 | 62 | 3 |
subtype3 | 32 | 1 |
subtype4 | 43 | 2 |
subtype5 | 82 | 8 |
subtype6 | 74 | 7 |
subtype7 | 12 | 0 |
Figure S63. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #9: 'RADIATION_THERAPY'

P value = 0.226 (Fisher's exact test), Q value = 0.4
Table S69. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 312 | 42 | 118 | 10 |
subtype1 | 49 | 10 | 17 | 1 |
subtype2 | 61 | 5 | 18 | 3 |
subtype3 | 28 | 2 | 15 | 0 |
subtype4 | 47 | 2 | 12 | 2 |
subtype5 | 62 | 16 | 28 | 1 |
subtype6 | 56 | 7 | 25 | 2 |
subtype7 | 9 | 0 | 3 | 1 |
Figure S64. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

P value = 0.00079 (Fisher's exact test), Q value = 0.0058
Table S70. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #11: 'RESIDUAL_TUMOR'
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 363 | 2 | 29 | 19 |
subtype1 | 57 | 1 | 1 | 3 |
subtype2 | 60 | 0 | 7 | 1 |
subtype3 | 33 | 0 | 6 | 2 |
subtype4 | 42 | 1 | 2 | 5 |
subtype5 | 90 | 0 | 1 | 2 |
subtype6 | 73 | 0 | 9 | 4 |
subtype7 | 8 | 0 | 3 | 2 |
Figure S65. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

P value = 0.246 (Kruskal-Wallis (anova)), Q value = 0.42
Table S71. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 460 | 2.1 (4.6) |
subtype1 | 73 | 3.2 (7.1) |
subtype2 | 84 | 2.1 (4.4) |
subtype3 | 43 | 2.8 (4.4) |
subtype4 | 59 | 2.2 (4.3) |
subtype5 | 103 | 1.5 (2.8) |
subtype6 | 87 | 1.7 (4.1) |
subtype7 | 11 | 1.3 (1.7) |
Figure S66. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

P value = 0.00284 (Fisher's exact test), Q value = 0.017
Table S72. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #13: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 12 | 51 | 246 |
subtype1 | 1 | 3 | 12 | 49 |
subtype2 | 0 | 0 | 9 | 43 |
subtype3 | 0 | 4 | 7 | 14 |
subtype4 | 0 | 1 | 8 | 35 |
subtype5 | 0 | 0 | 10 | 82 |
subtype6 | 0 | 4 | 4 | 21 |
subtype7 | 0 | 0 | 1 | 2 |
Figure S67. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #13: 'RACE'

P value = 0.0335 (Fisher's exact test), Q value = 0.11
Table S73. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #14: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 2 | 297 |
subtype1 | 0 | 65 |
subtype2 | 0 | 49 |
subtype3 | 1 | 20 |
subtype4 | 0 | 44 |
subtype5 | 0 | 91 |
subtype6 | 1 | 27 |
subtype7 | 0 | 1 |
Figure S68. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #14: 'ETHNICITY'

Table S74. Description of clustering approach #6: 'RPPA cHierClus subtypes'
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 236 | 166 | 86 |
P value = 0.817 (logrank test), Q value = 0.91
Table S75. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 474 | 98 | 0.0 - 140.4 (20.0) |
subtype1 | 231 | 42 | 0.0 - 135.7 (18.8) |
subtype2 | 161 | 41 | 0.1 - 140.4 (22.1) |
subtype3 | 82 | 15 | 0.0 - 88.2 (20.0) |
Figure S69. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'

P value = 0.125 (Kruskal-Wallis (anova)), Q value = 0.28
Table S76. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 487 | 66.6 (12.7) |
subtype1 | 236 | 65.8 (12.3) |
subtype2 | 165 | 66.7 (12.6) |
subtype3 | 86 | 68.4 (13.8) |
Figure S70. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

P value = 0.169 (Fisher's exact test), Q value = 0.34
Table S77. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'
nPatients | COLON | RECTUM |
---|---|---|
ALL | 357 | 131 |
subtype1 | 175 | 61 |
subtype2 | 126 | 40 |
subtype3 | 56 | 30 |
Figure S71. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

P value = 0.00408 (Fisher's exact test), Q value = 0.021
Table S78. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 1 | 27 | 148 | 9 | 2 | 24 | 15 | 69 | 42 | 46 | 20 | 2 |
subtype1 | 36 | 1 | 6 | 84 | 3 | 1 | 5 | 7 | 35 | 23 | 16 | 13 | 1 |
subtype2 | 28 | 0 | 9 | 47 | 4 | 1 | 12 | 6 | 20 | 15 | 15 | 5 | 1 |
subtype3 | 11 | 0 | 12 | 17 | 2 | 0 | 7 | 2 | 14 | 4 | 15 | 2 | 0 |
Figure S72. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

P value = 0.605 (Fisher's exact test), Q value = 0.8
Table S79. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 11 | 81 | 339 | 55 |
subtype1 | 5 | 35 | 168 | 26 |
subtype2 | 3 | 33 | 108 | 22 |
subtype3 | 3 | 13 | 63 | 7 |
Figure S73. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

P value = 0.595 (Fisher's exact test), Q value = 0.79
Table S80. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 274 | 122 | 89 |
subtype1 | 137 | 54 | 43 |
subtype2 | 91 | 41 | 33 |
subtype3 | 46 | 27 | 13 |
Figure S74. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

P value = 0.445 (Fisher's exact test), Q value = 0.65
Table S81. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 367 | 67 |
subtype1 | 180 | 31 |
subtype2 | 123 | 20 |
subtype3 | 64 | 16 |
Figure S75. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

P value = 0.647 (Fisher's exact test), Q value = 0.81
Table S82. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #8: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 233 | 255 |
subtype1 | 111 | 125 |
subtype2 | 77 | 89 |
subtype3 | 45 | 41 |
Figure S76. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #8: 'GENDER'

P value = 0.18 (Fisher's exact test), Q value = 0.35
Table S83. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #9: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 357 | 23 |
subtype1 | 177 | 10 |
subtype2 | 115 | 5 |
subtype3 | 65 | 8 |
Figure S77. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #9: 'RADIATION_THERAPY'

P value = 0.274 (Fisher's exact test), Q value = 0.46
Table S84. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 312 | 42 | 118 | 10 |
subtype1 | 147 | 27 | 57 | 4 |
subtype2 | 113 | 11 | 35 | 4 |
subtype3 | 52 | 4 | 26 | 2 |
Figure S78. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

P value = 0.00015 (Fisher's exact test), Q value = 0.0013
Table S85. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #11: 'RESIDUAL_TUMOR'
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 363 | 2 | 29 | 19 |
subtype1 | 192 | 1 | 4 | 7 |
subtype2 | 106 | 1 | 13 | 10 |
subtype3 | 65 | 0 | 12 | 2 |
Figure S79. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

P value = 0.679 (Kruskal-Wallis (anova)), Q value = 0.82
Table S86. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 460 | 2.1 (4.6) |
subtype1 | 224 | 2.1 (5.0) |
subtype2 | 153 | 2.4 (4.3) |
subtype3 | 83 | 1.7 (3.8) |
Figure S80. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

P value = 0.787 (Fisher's exact test), Q value = 0.9
Table S87. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #13: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 12 | 51 | 246 |
subtype1 | 1 | 6 | 27 | 144 |
subtype2 | 0 | 4 | 20 | 77 |
subtype3 | 0 | 2 | 4 | 25 |
Figure S81. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #13: 'RACE'

P value = 0.077 (Fisher's exact test), Q value = 0.2
Table S88. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #14: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 2 | 297 |
subtype1 | 0 | 173 |
subtype2 | 1 | 94 |
subtype3 | 1 | 30 |
Figure S82. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #14: 'ETHNICITY'

Table S89. Description of clustering approach #7: 'RNAseq CNMF subtypes'
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 148 | 142 | 131 | 199 |
P value = 0.0987 (logrank test), Q value = 0.23
Table S90. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 602 | 121 | 0.0 - 148.0 (20.0) |
subtype1 | 144 | 37 | 0.1 - 140.4 (21.0) |
subtype2 | 141 | 23 | 0.0 - 135.7 (20.0) |
subtype3 | 127 | 32 | 0.1 - 148.0 (17.8) |
subtype4 | 190 | 29 | 0.0 - 117.1 (21.5) |
Figure S83. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #1: 'Time to Death'

P value = 0.00283 (Kruskal-Wallis (anova)), Q value = 0.017
Table S91. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 618 | 66.4 (12.7) |
subtype1 | 148 | 63.8 (12.3) |
subtype2 | 141 | 66.4 (13.4) |
subtype3 | 130 | 65.5 (13.2) |
subtype4 | 199 | 68.8 (11.9) |
Figure S84. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

P value = 0.0959 (Fisher's exact test), Q value = 0.23
Table S92. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'
nPatients | COLON | RECTUM |
---|---|---|
ALL | 453 | 163 |
subtype1 | 103 | 45 |
subtype2 | 110 | 30 |
subtype3 | 103 | 28 |
subtype4 | 137 | 60 |
Figure S85. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

P value = 0.00386 (Fisher's exact test), Q value = 0.02
Table S93. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 104 | 1 | 37 | 178 | 11 | 3 | 27 | 18 | 83 | 54 | 62 | 26 | 2 |
subtype1 | 23 | 0 | 7 | 37 | 2 | 2 | 4 | 4 | 24 | 11 | 14 | 13 | 0 |
subtype2 | 29 | 1 | 11 | 42 | 2 | 1 | 7 | 6 | 19 | 7 | 7 | 6 | 2 |
subtype3 | 12 | 0 | 5 | 44 | 2 | 0 | 3 | 3 | 18 | 18 | 16 | 6 | 0 |
subtype4 | 40 | 0 | 14 | 55 | 5 | 0 | 13 | 5 | 22 | 18 | 25 | 1 | 0 |
Figure S86. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

P value = 0.0414 (Fisher's exact test), Q value = 0.13
Table S94. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 20 | 106 | 423 | 69 |
subtype1 | 6 | 25 | 99 | 17 |
subtype2 | 4 | 30 | 94 | 13 |
subtype3 | 1 | 13 | 94 | 23 |
subtype4 | 9 | 38 | 136 | 16 |
Figure S87. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

P value = 0.112 (Fisher's exact test), Q value = 0.26
Table S95. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 352 | 150 | 115 |
subtype1 | 83 | 40 | 23 |
subtype2 | 89 | 34 | 19 |
subtype3 | 64 | 31 | 35 |
subtype4 | 116 | 45 | 38 |
Figure S88. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

P value = 0.0843 (Fisher's exact test), Q value = 0.21
Table S96. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 458 | 87 |
subtype1 | 96 | 27 |
subtype2 | 101 | 13 |
subtype3 | 91 | 21 |
subtype4 | 170 | 26 |
Figure S89. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

P value = 0.608 (Fisher's exact test), Q value = 0.8
Table S97. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #8: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 289 | 331 |
subtype1 | 64 | 84 |
subtype2 | 68 | 74 |
subtype3 | 58 | 73 |
subtype4 | 99 | 100 |
Figure S90. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #8: 'GENDER'

P value = 0.0673 (Fisher's exact test), Q value = 0.17
Table S98. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #9: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 454 | 29 |
subtype1 | 97 | 6 |
subtype2 | 111 | 6 |
subtype3 | 105 | 2 |
subtype4 | 141 | 15 |
Figure S91. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #9: 'RADIATION_THERAPY'

P value = 2e-05 (Fisher's exact test), Q value = 0.00022
Table S99. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 388 | 61 | 147 | 13 |
subtype1 | 99 | 2 | 45 | 0 |
subtype2 | 85 | 23 | 24 | 5 |
subtype3 | 85 | 18 | 25 | 3 |
subtype4 | 119 | 18 | 53 | 5 |
Figure S92. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00022
Table S100. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #11: 'RESIDUAL_TUMOR'
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 449 | 5 | 36 | 30 |
subtype1 | 90 | 1 | 7 | 10 |
subtype2 | 94 | 2 | 3 | 9 |
subtype3 | 94 | 1 | 4 | 11 |
subtype4 | 171 | 1 | 22 | 0 |
Figure S93. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

P value = 0.0494 (Kruskal-Wallis (anova)), Q value = 0.14
Table S101. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 583 | 2.2 (4.7) |
subtype1 | 133 | 1.9 (3.9) |
subtype2 | 132 | 1.8 (4.1) |
subtype3 | 121 | 3.2 (6.5) |
subtype4 | 197 | 2.1 (4.3) |
Figure S94. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

P value = 0.863 (Fisher's exact test), Q value = 0.92
Table S102. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #13: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 12 | 64 | 294 |
subtype1 | 0 | 4 | 21 | 96 |
subtype2 | 0 | 4 | 22 | 77 |
subtype3 | 1 | 4 | 17 | 101 |
subtype4 | 0 | 0 | 4 | 20 |
Figure S95. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #13: 'RACE'

P value = 0.237 (Fisher's exact test), Q value = 0.41
Table S103. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #14: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 5 | 349 |
subtype1 | 4 | 112 |
subtype2 | 0 | 97 |
subtype3 | 1 | 116 |
subtype4 | 0 | 24 |
Figure S96. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #14: 'ETHNICITY'

Table S104. Description of clustering approach #8: 'RNAseq cHierClus subtypes'
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
---|---|---|---|---|---|---|---|
Number of samples | 80 | 86 | 64 | 57 | 90 | 140 | 103 |
P value = 0.445 (logrank test), Q value = 0.65
Table S105. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 602 | 121 | 0.0 - 148.0 (20.0) |
subtype1 | 79 | 20 | 0.1 - 148.0 (18.2) |
subtype2 | 85 | 16 | 0.8 - 133.2 (19.1) |
subtype3 | 61 | 16 | 0.1 - 135.7 (20.0) |
subtype4 | 56 | 7 | 1.4 - 91.8 (20.9) |
subtype5 | 90 | 20 | 0.4 - 129.3 (16.6) |
subtype6 | 131 | 20 | 0.0 - 117.1 (21.0) |
subtype7 | 100 | 22 | 0.0 - 64.0 (24.0) |
Figure S97. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'

P value = 0.00104 (Kruskal-Wallis (anova)), Q value = 0.0073
Table S106. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 618 | 66.4 (12.7) |
subtype1 | 80 | 64.5 (13.0) |
subtype2 | 86 | 65.0 (13.4) |
subtype3 | 62 | 64.7 (15.4) |
subtype4 | 57 | 64.7 (12.8) |
subtype5 | 90 | 63.9 (11.6) |
subtype6 | 140 | 68.0 (10.9) |
subtype7 | 103 | 70.8 (12.2) |
Figure S98. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013
Table S107. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'
nPatients | COLON | RECTUM |
---|---|---|
ALL | 453 | 163 |
subtype1 | 58 | 22 |
subtype2 | 73 | 13 |
subtype3 | 60 | 4 |
subtype4 | 32 | 23 |
subtype5 | 59 | 31 |
subtype6 | 88 | 51 |
subtype7 | 83 | 19 |
Figure S99. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00031
Table S108. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 104 | 1 | 37 | 178 | 11 | 3 | 27 | 18 | 83 | 54 | 62 | 26 | 2 |
subtype1 | 14 | 0 | 1 | 25 | 1 | 1 | 1 | 3 | 12 | 9 | 5 | 5 | 0 |
subtype2 | 15 | 1 | 6 | 24 | 1 | 0 | 3 | 4 | 14 | 5 | 5 | 5 | 1 |
subtype3 | 13 | 0 | 4 | 28 | 1 | 0 | 1 | 1 | 4 | 6 | 2 | 1 | 1 |
subtype4 | 8 | 0 | 3 | 8 | 1 | 1 | 5 | 4 | 11 | 3 | 6 | 5 | 0 |
subtype5 | 7 | 0 | 3 | 26 | 1 | 1 | 1 | 1 | 17 | 11 | 9 | 9 | 0 |
subtype6 | 28 | 0 | 7 | 37 | 1 | 0 | 8 | 4 | 16 | 14 | 25 | 0 | 0 |
subtype7 | 19 | 0 | 13 | 30 | 5 | 0 | 8 | 1 | 9 | 6 | 10 | 1 | 0 |
Figure S100. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

P value = 0.68 (Fisher's exact test), Q value = 0.82
Table S109. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 20 | 106 | 423 | 69 |
subtype1 | 2 | 14 | 55 | 9 |
subtype2 | 5 | 15 | 53 | 12 |
subtype3 | 2 | 11 | 44 | 7 |
subtype4 | 1 | 9 | 40 | 7 |
subtype5 | 0 | 10 | 66 | 13 |
subtype6 | 6 | 30 | 94 | 10 |
subtype7 | 4 | 17 | 71 | 11 |
Figure S101. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

P value = 0.0149 (Fisher's exact test), Q value = 0.059
Table S110. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 352 | 150 | 115 |
subtype1 | 44 | 18 | 17 |
subtype2 | 52 | 23 | 11 |
subtype3 | 46 | 9 | 9 |
subtype4 | 26 | 22 | 9 |
subtype5 | 39 | 27 | 22 |
subtype6 | 77 | 34 | 29 |
subtype7 | 68 | 17 | 18 |
Figure S102. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

P value = 0.101 (Fisher's exact test), Q value = 0.24
Table S111. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 458 | 87 |
subtype1 | 56 | 10 |
subtype2 | 57 | 8 |
subtype3 | 46 | 4 |
subtype4 | 34 | 11 |
subtype5 | 61 | 18 |
subtype6 | 113 | 25 |
subtype7 | 91 | 11 |
Figure S103. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

P value = 0.361 (Fisher's exact test), Q value = 0.55
Table S112. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #8: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 289 | 331 |
subtype1 | 37 | 43 |
subtype2 | 41 | 45 |
subtype3 | 29 | 35 |
subtype4 | 18 | 39 |
subtype5 | 43 | 47 |
subtype6 | 68 | 72 |
subtype7 | 53 | 50 |
Figure S104. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #8: 'GENDER'

P value = 0.726 (Fisher's exact test), Q value = 0.86
Table S113. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #9: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 454 | 29 |
subtype1 | 48 | 3 |
subtype2 | 71 | 2 |
subtype3 | 48 | 2 |
subtype4 | 45 | 3 |
subtype5 | 69 | 4 |
subtype6 | 96 | 10 |
subtype7 | 77 | 5 |
Figure S105. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #9: 'RADIATION_THERAPY'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013
Table S114. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 388 | 61 | 147 | 13 |
subtype1 | 55 | 2 | 22 | 0 |
subtype2 | 58 | 14 | 11 | 2 |
subtype3 | 47 | 12 | 3 | 1 |
subtype4 | 30 | 2 | 22 | 1 |
subtype5 | 53 | 6 | 30 | 1 |
subtype6 | 85 | 3 | 50 | 0 |
subtype7 | 60 | 22 | 9 | 8 |
Figure S106. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013
Table S115. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #11: 'RESIDUAL_TUMOR'
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 449 | 5 | 36 | 30 |
subtype1 | 45 | 0 | 2 | 8 |
subtype2 | 58 | 0 | 1 | 4 |
subtype3 | 41 | 1 | 1 | 9 |
subtype4 | 34 | 2 | 2 | 2 |
subtype5 | 66 | 0 | 0 | 7 |
subtype6 | 115 | 2 | 22 | 0 |
subtype7 | 90 | 0 | 8 | 0 |
Figure S107. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

P value = 0.0207 (Kruskal-Wallis (anova)), Q value = 0.074
Table S116. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 583 | 2.2 (4.7) |
subtype1 | 72 | 2.1 (3.2) |
subtype2 | 78 | 1.8 (4.5) |
subtype3 | 57 | 1.4 (3.3) |
subtype4 | 53 | 2.6 (5.1) |
subtype5 | 82 | 3.1 (6.5) |
subtype6 | 138 | 2.2 (4.4) |
subtype7 | 103 | 2.2 (5.1) |
Figure S108. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

P value = 0.0561 (Fisher's exact test), Q value = 0.16
Table S117. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #13: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 12 | 64 | 294 |
subtype1 | 0 | 3 | 13 | 59 |
subtype2 | 0 | 0 | 23 | 49 |
subtype3 | 0 | 4 | 8 | 49 |
subtype4 | 0 | 1 | 4 | 43 |
subtype5 | 1 | 4 | 11 | 71 |
subtype6 | 0 | 0 | 4 | 13 |
subtype7 | 0 | 0 | 1 | 10 |
Figure S109. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #13: 'RACE'

P value = 0.937 (Fisher's exact test), Q value = 0.98
Table S118. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #14: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 5 | 349 |
subtype1 | 1 | 70 |
subtype2 | 2 | 67 |
subtype3 | 1 | 58 |
subtype4 | 0 | 45 |
subtype5 | 1 | 81 |
subtype6 | 0 | 17 |
subtype7 | 0 | 11 |
Figure S110. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #14: 'ETHNICITY'

Table S119. Description of clustering approach #9: 'MIRSEQ CNMF'
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 212 | 96 | 241 |
P value = 0.0609 (logrank test), Q value = 0.16
Table S120. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 531 | 110 | 0.0 - 148.0 (21.0) |
subtype1 | 209 | 42 | 0.1 - 148.0 (20.9) |
subtype2 | 94 | 24 | 0.1 - 109.3 (17.5) |
subtype3 | 228 | 44 | 0.0 - 117.1 (22.2) |
Figure S111. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #1: 'Time to Death'

P value = 0.00875 (Kruskal-Wallis (anova)), Q value = 0.04
Table S121. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 548 | 66.8 (12.7) |
subtype1 | 211 | 65.9 (12.5) |
subtype2 | 96 | 64.0 (13.8) |
subtype3 | 241 | 68.8 (12.1) |
Figure S112. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

P value = 0.0396 (Fisher's exact test), Q value = 0.12
Table S122. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'
nPatients | COLON | RECTUM |
---|---|---|
ALL | 405 | 140 |
subtype1 | 150 | 61 |
subtype2 | 80 | 15 |
subtype3 | 175 | 64 |
Figure S113. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

P value = 0.00028 (Fisher's exact test), Q value = 0.0021
Table S123. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 94 | 1 | 36 | 154 | 10 | 2 | 27 | 13 | 72 | 46 | 57 | 22 | 1 |
subtype1 | 32 | 1 | 8 | 67 | 4 | 2 | 8 | 7 | 35 | 14 | 16 | 10 | 1 |
subtype2 | 9 | 0 | 5 | 26 | 0 | 0 | 3 | 2 | 16 | 14 | 7 | 8 | 0 |
subtype3 | 53 | 0 | 23 | 61 | 6 | 0 | 16 | 4 | 21 | 18 | 34 | 4 | 0 |
Figure S114. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

P value = 0.0969 (Fisher's exact test), Q value = 0.23
Table S124. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 20 | 94 | 377 | 56 |
subtype1 | 8 | 32 | 152 | 18 |
subtype2 | 2 | 10 | 69 | 15 |
subtype3 | 10 | 52 | 156 | 23 |
Figure S115. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

P value = 0.0152 (Fisher's exact test), Q value = 0.059
Table S125. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 312 | 134 | 100 |
subtype1 | 120 | 59 | 31 |
subtype2 | 43 | 29 | 23 |
subtype3 | 149 | 46 | 46 |
Figure S116. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

P value = 0.817 (Fisher's exact test), Q value = 0.91
Table S126. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 412 | 78 |
subtype1 | 149 | 26 |
subtype2 | 65 | 14 |
subtype3 | 198 | 38 |
Figure S117. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

P value = 0.543 (Fisher's exact test), Q value = 0.74
Table S127. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #8: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 257 | 292 |
subtype1 | 102 | 110 |
subtype2 | 40 | 56 |
subtype3 | 115 | 126 |
Figure S118. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #8: 'GENDER'

P value = 0.71 (Fisher's exact test), Q value = 0.85
Table S128. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #9: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 399 | 25 |
subtype1 | 144 | 7 |
subtype2 | 73 | 5 |
subtype3 | 182 | 13 |
Figure S119. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #9: 'RADIATION_THERAPY'

P value = 5e-05 (Fisher's exact test), Q value = 0.00049
Table S129. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 348 | 53 | 127 | 10 |
subtype1 | 138 | 9 | 60 | 1 |
subtype2 | 60 | 20 | 13 | 2 |
subtype3 | 150 | 24 | 54 | 7 |
Figure S120. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013
Table S130. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #11: 'RESIDUAL_TUMOR'
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 384 | 5 | 36 | 26 |
subtype1 | 121 | 2 | 5 | 17 |
subtype2 | 66 | 0 | 2 | 7 |
subtype3 | 197 | 3 | 29 | 2 |
Figure S121. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

P value = 0.0488 (Kruskal-Wallis (anova)), Q value = 0.14
Table S131. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 514 | 2.2 (4.7) |
subtype1 | 189 | 1.8 (3.5) |
subtype2 | 89 | 3.3 (7.1) |
subtype3 | 236 | 2.1 (4.4) |
Figure S122. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

P value = 0.659 (Fisher's exact test), Q value = 0.81
Table S132. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #13: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 12 | 26 | 280 |
subtype1 | 0 | 7 | 14 | 171 |
subtype2 | 1 | 4 | 7 | 73 |
subtype3 | 0 | 1 | 5 | 36 |
Figure S123. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #13: 'RACE'

P value = 1 (Fisher's exact test), Q value = 1
Table S133. Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #14: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 2 | 305 |
subtype1 | 2 | 184 |
subtype2 | 0 | 80 |
subtype3 | 0 | 41 |
Figure S124. Get High-res Image Clustering Approach #9: 'MIRSEQ CNMF' versus Clinical Feature #14: 'ETHNICITY'

Table S134. Description of clustering approach #10: 'MIRSEQ CHIERARCHICAL'
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 229 | 144 | 176 |
P value = 0.846 (logrank test), Q value = 0.92
Table S135. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 531 | 110 | 0.0 - 148.0 (21.0) |
subtype1 | 226 | 51 | 0.1 - 140.4 (19.3) |
subtype2 | 138 | 28 | 0.0 - 148.0 (20.7) |
subtype3 | 167 | 31 | 0.0 - 109.3 (25.0) |
Figure S125. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #1: 'Time to Death'

P value = 0.00428 (Kruskal-Wallis (anova)), Q value = 0.021
Table S136. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 548 | 66.8 (12.7) |
subtype1 | 228 | 65.8 (12.8) |
subtype2 | 144 | 65.1 (13.0) |
subtype3 | 176 | 69.6 (11.9) |
Figure S126. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

P value = 0.261 (Fisher's exact test), Q value = 0.44
Table S137. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'
nPatients | COLON | RECTUM |
---|---|---|
ALL | 405 | 140 |
subtype1 | 176 | 51 |
subtype2 | 100 | 43 |
subtype3 | 129 | 46 |
Figure S127. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

P value = 0.012 (Fisher's exact test), Q value = 0.05
Table S138. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 94 | 1 | 36 | 154 | 10 | 2 | 27 | 13 | 72 | 46 | 57 | 22 | 1 |
subtype1 | 36 | 0 | 10 | 78 | 4 | 1 | 7 | 6 | 31 | 19 | 13 | 13 | 1 |
subtype2 | 22 | 1 | 6 | 34 | 2 | 1 | 8 | 5 | 21 | 14 | 23 | 4 | 0 |
subtype3 | 36 | 0 | 20 | 42 | 4 | 0 | 12 | 2 | 20 | 13 | 21 | 5 | 0 |
Figure S128. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

P value = 0.903 (Fisher's exact test), Q value = 0.96
Table S139. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 20 | 94 | 377 | 56 |
subtype1 | 8 | 36 | 159 | 25 |
subtype2 | 6 | 22 | 101 | 14 |
subtype3 | 6 | 36 | 117 | 17 |
Figure S129. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

P value = 0.147 (Fisher's exact test), Q value = 0.31
Table S140. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 312 | 134 | 100 |
subtype1 | 137 | 54 | 36 |
subtype2 | 69 | 42 | 32 |
subtype3 | 106 | 38 | 32 |
Figure S130. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

P value = 0.192 (Fisher's exact test), Q value = 0.37
Table S141. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 412 | 78 |
subtype1 | 163 | 25 |
subtype2 | 103 | 27 |
subtype3 | 146 | 26 |
Figure S131. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

P value = 0.52 (Fisher's exact test), Q value = 0.72
Table S142. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #8: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 257 | 292 |
subtype1 | 101 | 128 |
subtype2 | 72 | 72 |
subtype3 | 84 | 92 |
Figure S132. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #8: 'GENDER'

P value = 0.84 (Fisher's exact test), Q value = 0.92
Table S143. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #9: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 399 | 25 |
subtype1 | 164 | 11 |
subtype2 | 98 | 7 |
subtype3 | 137 | 7 |
Figure S133. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #9: 'RADIATION_THERAPY'

P value = 0.237 (Fisher's exact test), Q value = 0.41
Table S144. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 348 | 53 | 127 | 10 |
subtype1 | 149 | 25 | 49 | 2 |
subtype2 | 90 | 8 | 40 | 3 |
subtype3 | 109 | 20 | 38 | 5 |
Figure S134. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

P value = 0.00013 (Fisher's exact test), Q value = 0.0012
Table S145. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #11: 'RESIDUAL_TUMOR'
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 384 | 5 | 36 | 26 |
subtype1 | 142 | 2 | 4 | 17 |
subtype2 | 95 | 1 | 15 | 7 |
subtype3 | 147 | 2 | 17 | 2 |
Figure S135. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

P value = 0.127 (Kruskal-Wallis (anova)), Q value = 0.28
Table S146. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 514 | 2.2 (4.7) |
subtype1 | 212 | 1.9 (3.9) |
subtype2 | 129 | 2.5 (5.4) |
subtype3 | 173 | 2.3 (5.2) |
Figure S136. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

P value = 0.791 (Fisher's exact test), Q value = 0.9
Table S147. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #13: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 12 | 26 | 280 |
subtype1 | 1 | 8 | 15 | 181 |
subtype2 | 0 | 4 | 7 | 68 |
subtype3 | 0 | 0 | 4 | 31 |
Figure S137. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #13: 'RACE'

P value = 0.594 (Fisher's exact test), Q value = 0.79
Table S148. Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #14: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 2 | 305 |
subtype1 | 1 | 195 |
subtype2 | 1 | 75 |
subtype3 | 0 | 35 |
Figure S138. Get High-res Image Clustering Approach #10: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #14: 'ETHNICITY'

Table S149. Description of clustering approach #11: 'MIRseq Mature CNMF subtypes'
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 24 | 20 | 29 | 28 | 18 | 17 |
P value = 0.855 (logrank test), Q value = 0.92
Table S150. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 134 | 39 | 0.1 - 140.4 (20.6) |
subtype1 | 24 | 6 | 0.2 - 130.7 (22.6) |
subtype2 | 19 | 6 | 0.1 - 74.8 (16.2) |
subtype3 | 29 | 7 | 0.4 - 129.3 (24.1) |
subtype4 | 27 | 10 | 1.4 - 140.4 (13.3) |
subtype5 | 18 | 5 | 1.9 - 139.2 (20.0) |
subtype6 | 17 | 5 | 0.7 - 131.5 (21.4) |
Figure S139. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #1: 'Time to Death'

P value = 0.201 (Kruskal-Wallis (anova)), Q value = 0.38
Table S151. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 135 | 64.9 (12.6) |
subtype1 | 24 | 68.0 (12.5) |
subtype2 | 20 | 62.6 (14.2) |
subtype3 | 29 | 61.9 (12.3) |
subtype4 | 28 | 66.4 (10.9) |
subtype5 | 18 | 62.4 (12.8) |
subtype6 | 16 | 68.6 (13.2) |
Figure S140. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013
Table S152. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'
nPatients | COLON | RECTUM |
---|---|---|
ALL | 85 | 50 |
subtype1 | 13 | 11 |
subtype2 | 20 | 0 |
subtype3 | 6 | 22 |
subtype4 | 16 | 12 |
subtype5 | 16 | 2 |
subtype6 | 14 | 3 |
Figure S141. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

P value = 0.194 (Fisher's exact test), Q value = 0.37
Table S153. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 15 | 7 | 39 | 1 | 1 | 2 | 4 | 21 | 14 | 13 | 9 |
subtype1 | 6 | 1 | 7 | 0 | 0 | 1 | 0 | 4 | 1 | 2 | 1 |
subtype2 | 2 | 1 | 4 | 0 | 0 | 0 | 0 | 4 | 4 | 4 | 1 |
subtype3 | 0 | 1 | 8 | 0 | 0 | 0 | 1 | 5 | 4 | 4 | 4 |
subtype4 | 1 | 0 | 10 | 0 | 1 | 1 | 3 | 4 | 2 | 0 | 1 |
subtype5 | 2 | 2 | 4 | 1 | 0 | 0 | 0 | 1 | 1 | 3 | 2 |
subtype6 | 4 | 2 | 6 | 0 | 0 | 0 | 0 | 3 | 2 | 0 | 0 |
Figure S142. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

P value = 0.143 (Fisher's exact test), Q value = 0.31
Table S154. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 4 | 16 | 100 | 15 |
subtype1 | 2 | 5 | 15 | 2 |
subtype2 | 0 | 2 | 16 | 2 |
subtype3 | 0 | 0 | 26 | 2 |
subtype4 | 1 | 3 | 21 | 3 |
subtype5 | 0 | 3 | 10 | 5 |
subtype6 | 1 | 3 | 12 | 1 |
Figure S143. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

P value = 0.214 (Fisher's exact test), Q value = 0.4
Table S155. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 65 | 39 | 30 |
subtype1 | 13 | 6 | 5 |
subtype2 | 7 | 5 | 8 |
subtype3 | 9 | 10 | 8 |
subtype4 | 13 | 10 | 5 |
subtype5 | 10 | 6 | 2 |
subtype6 | 13 | 2 | 2 |
Figure S144. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

P value = 0.0254 (Fisher's exact test), Q value = 0.087
Table S156. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 87 | 21 |
subtype1 | 17 | 2 |
subtype2 | 11 | 5 |
subtype3 | 17 | 7 |
subtype4 | 18 | 2 |
subtype5 | 8 | 5 |
subtype6 | 16 | 0 |
Figure S145. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

P value = 0.857 (Fisher's exact test), Q value = 0.92
Table S157. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #8: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 58 | 78 |
subtype1 | 8 | 16 |
subtype2 | 9 | 11 |
subtype3 | 15 | 14 |
subtype4 | 12 | 16 |
subtype5 | 7 | 11 |
subtype6 | 7 | 10 |
Figure S146. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #8: 'GENDER'

P value = 0.361 (Fisher's exact test), Q value = 0.55
Table S158. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #9: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 93 | 6 |
subtype1 | 16 | 2 |
subtype2 | 17 | 0 |
subtype3 | 18 | 3 |
subtype4 | 15 | 1 |
subtype5 | 14 | 0 |
subtype6 | 13 | 0 |
Figure S147. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #9: 'RADIATION_THERAPY'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013
Table S159. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 74 | 9 | 49 | 1 |
subtype1 | 13 | 0 | 11 | 0 |
subtype2 | 16 | 4 | 0 | 0 |
subtype3 | 6 | 0 | 22 | 0 |
subtype4 | 13 | 1 | 11 | 1 |
subtype5 | 12 | 4 | 2 | 0 |
subtype6 | 14 | 0 | 3 | 0 |
Figure S148. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

P value = 0.534 (Fisher's exact test), Q value = 0.74
Table S160. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #11: 'RESIDUAL_TUMOR'
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 73 | 1 | 2 | 7 |
subtype1 | 12 | 0 | 0 | 2 |
subtype2 | 14 | 0 | 0 | 0 |
subtype3 | 18 | 0 | 2 | 2 |
subtype4 | 11 | 1 | 0 | 0 |
subtype5 | 9 | 0 | 0 | 1 |
subtype6 | 9 | 0 | 0 | 2 |
Figure S149. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

P value = 0.0318 (Kruskal-Wallis (anova)), Q value = 0.1
Table S161. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 125 | 2.9 (6.2) |
subtype1 | 23 | 2.6 (4.4) |
subtype2 | 19 | 6.9 (11.6) |
subtype3 | 25 | 3.1 (4.7) |
subtype4 | 26 | 2.0 (5.4) |
subtype5 | 17 | 1.4 (3.0) |
subtype6 | 15 | 1.1 (2.3) |
Figure S150. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

P value = 0.218 (Fisher's exact test), Q value = 0.4
Table S162. Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #13: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 3 | 8 | 117 |
subtype1 | 0 | 0 | 2 | 20 |
subtype2 | 1 | 0 | 2 | 16 |
subtype3 | 0 | 1 | 0 | 25 |
subtype4 | 0 | 0 | 1 | 27 |
subtype5 | 0 | 0 | 2 | 15 |
subtype6 | 0 | 2 | 1 | 14 |
Figure S151. Get High-res Image Clustering Approach #11: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #13: 'RACE'

Table S163. Description of clustering approach #12: 'MIRseq Mature cHierClus subtypes'
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 55 | 15 | 34 | 32 |
P value = 0.503 (logrank test), Q value = 0.72
Table S164. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 134 | 39 | 0.1 - 140.4 (20.6) |
subtype1 | 54 | 19 | 0.1 - 100.0 (20.0) |
subtype2 | 15 | 3 | 0.7 - 129.3 (16.3) |
subtype3 | 34 | 9 | 0.2 - 131.5 (24.4) |
subtype4 | 31 | 8 | 0.4 - 140.4 (17.5) |
Figure S152. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'

P value = 0.516 (Kruskal-Wallis (anova)), Q value = 0.72
Table S165. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 135 | 64.9 (12.6) |
subtype1 | 55 | 64.6 (13.8) |
subtype2 | 15 | 61.7 (12.3) |
subtype3 | 33 | 67.3 (12.6) |
subtype4 | 32 | 64.3 (10.5) |
Figure S153. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013
Table S166. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'
nPatients | COLON | RECTUM |
---|---|---|
ALL | 85 | 50 |
subtype1 | 50 | 5 |
subtype2 | 5 | 9 |
subtype3 | 18 | 16 |
subtype4 | 12 | 20 |
Figure S154. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

P value = 0.767 (Fisher's exact test), Q value = 0.89
Table S167. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 15 | 7 | 39 | 1 | 1 | 2 | 4 | 21 | 14 | 13 | 9 |
subtype1 | 9 | 3 | 15 | 1 | 0 | 0 | 0 | 7 | 7 | 6 | 2 |
subtype2 | 0 | 1 | 5 | 0 | 0 | 0 | 1 | 4 | 1 | 1 | 2 |
subtype3 | 4 | 2 | 9 | 0 | 1 | 1 | 2 | 7 | 3 | 2 | 1 |
subtype4 | 2 | 1 | 10 | 0 | 0 | 1 | 1 | 3 | 3 | 4 | 4 |
Figure S155. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

P value = 0.441 (Fisher's exact test), Q value = 0.65
Table S168. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 4 | 16 | 100 | 15 |
subtype1 | 1 | 9 | 36 | 9 |
subtype2 | 0 | 0 | 14 | 1 |
subtype3 | 2 | 5 | 25 | 2 |
subtype4 | 1 | 2 | 25 | 3 |
Figure S156. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

P value = 0.749 (Fisher's exact test), Q value = 0.88
Table S169. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 65 | 39 | 30 |
subtype1 | 31 | 12 | 12 |
subtype2 | 6 | 5 | 4 |
subtype3 | 14 | 12 | 8 |
subtype4 | 14 | 10 | 6 |
Figure S157. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

P value = 0.473 (Fisher's exact test), Q value = 0.68
Table S170. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 87 | 21 |
subtype1 | 34 | 8 |
subtype2 | 10 | 2 |
subtype3 | 23 | 3 |
subtype4 | 20 | 8 |
Figure S158. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

P value = 0.323 (Fisher's exact test), Q value = 0.52
Table S171. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #8: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 58 | 78 |
subtype1 | 23 | 32 |
subtype2 | 9 | 6 |
subtype3 | 11 | 23 |
subtype4 | 15 | 17 |
Figure S159. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #8: 'GENDER'

P value = 0.00861 (Fisher's exact test), Q value = 0.04
Table S172. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #9: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 93 | 6 |
subtype1 | 48 | 0 |
subtype2 | 7 | 2 |
subtype3 | 20 | 3 |
subtype4 | 18 | 1 |
Figure S160. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #9: 'RADIATION_THERAPY'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013
Table S173. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 74 | 9 | 49 | 1 |
subtype1 | 42 | 8 | 5 | 0 |
subtype2 | 5 | 0 | 9 | 0 |
subtype3 | 18 | 0 | 15 | 1 |
subtype4 | 9 | 1 | 20 | 0 |
Figure S161. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

P value = 0.357 (Fisher's exact test), Q value = 0.55
Table S174. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #11: 'RESIDUAL_TUMOR'
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 73 | 1 | 2 | 7 |
subtype1 | 33 | 0 | 0 | 3 |
subtype2 | 11 | 0 | 0 | 1 |
subtype3 | 13 | 1 | 0 | 2 |
subtype4 | 16 | 0 | 2 | 1 |
Figure S162. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

P value = 0.348 (Kruskal-Wallis (anova)), Q value = 0.55
Table S175. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 125 | 2.9 (6.2) |
subtype1 | 51 | 3.0 (7.7) |
subtype2 | 14 | 3.6 (5.8) |
subtype3 | 32 | 3.3 (5.8) |
subtype4 | 28 | 1.8 (2.9) |
Figure S163. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

P value = 0.795 (Fisher's exact test), Q value = 0.9
Table S176. Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #13: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 3 | 8 | 117 |
subtype1 | 1 | 1 | 5 | 46 |
subtype2 | 0 | 1 | 0 | 13 |
subtype3 | 0 | 1 | 2 | 30 |
subtype4 | 0 | 0 | 1 | 28 |
Figure S164. Get High-res Image Clustering Approach #12: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #13: 'RACE'

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Cluster data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/COADREAD-TP/20147373/COADREAD-TP.mergedcluster.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/COADREAD-TP/19775152/COADREAD-TP.merged_data.txt
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Number of patients = 625
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Number of clustering approaches = 12
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Number of selected clinical features = 14
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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.