Colon/Rectal Adenocarcinoma: Correlation between molecular cancer subtypes and selected clinical features
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
Overview
Introduction

This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.

Summary

Testing the association between subtypes identified by 10 different clustering approaches and 11 clinical features across 588 patients, 33 significant findings detected with P value < 0.05.

- CNMF clustering analysis on array-based mRNA expression data identified 4 subtypes that correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.

- Consensus hierarchical clustering analysis on array-based mRNA expression data identified 3 subtypes that correlate to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

- 4 subtypes identified in current cancer cohort by 'CN CNMF'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.

- 3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', and 'HISTOLOGICAL.TYPE'.

- CNMF clustering analysis on RPPA data identified 4 subtypes that correlate to 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.

- Consensus hierarchical clustering analysis on RPPA data identified 4 subtypes that correlate to 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.

- CNMF clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that correlate to 'HISTOLOGICAL.TYPE'.

- Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that correlate to 'HISTOLOGICAL.TYPE'.

- CNMF clustering analysis on sequencing-based miR expression data identified 3 subtypes that correlate to 'AGE', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'NEOADJUVANT.THERAPY'.

- Consensus hierarchical clustering analysis on sequencing-based miR expression data identified 3 subtypes that correlate to 'AGE', 'HISTOLOGICAL.TYPE', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'NEOADJUVANT.THERAPY'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between subtypes identified by 10 different clustering approaches and 11 clinical features. Shown in the table are P values from statistical tests. Thresholded by P value < 0.05, 33 significant findings detected.

Clinical Features | Statistical Tests | mRNA CNMF subtypes | mRNA cHierClus subtypes | CN CNMF | METHLYATION CNMF | RPPA CNMF subtypes | RPPA cHierClus subtypes | RNAseq CNMF subtypes | RNAseq cHierClus subtypes | MIRseq CNMF subtypes | MIRseq cHierClus subtypes
Time to Death | logrank test | 0.145 | 0.805 | 0.372 | 0.918 | 0.273 | 0.0945 | 0.12 | 0.176 | 0.238 | 0.598
AGE | ANOVA | 0.596 | 0.148 | 0.628 | 0.00372 | 0.467 | 0.505 | 0.416 | 0.884 | 0.00171 | 0.00388
PRIMARY SITE OF DISEASE | Fisher's exact test | 0.0126 | 0.035 | 7.44e-05 | 0.00624 | 0.469 | 0.258 | 0.111 | 0.265 | 0.565 | 0.0614
GENDER | Fisher's exact test | 0.072 | 0.796 | 0.804 | 0.031 | 0.474 | 0.121 | 0.869 | 0.924 | 0.471 | 0.683
HISTOLOGICAL TYPE | Chi-square test | 6.39e-07 | 3.6e-08 | 4.28e-13 | 0.00456 | 0.447 | 0.272 | 0.0132 | 0.00215 | 0.0981 | 0.0326
PATHOLOGY T | Chi-square test | 0.184 | 0.866 | 0.934 | 0.569 | 0.455 | 0.527 | 0.439 | 0.71 | 0.0706 | 0.15
PATHOLOGY N | Chi-square test | 0.00595 | 0.65 | 0.00155 | 0.429 | 0.0253 | 0.0289 | 0.872 | 0.969 | 0.0069 | 0.199
PATHOLOGICSPREAD(M) | Chi-square test | 0.00173 | 0.498 | 0.2 | 0.686 | 0.0189 | 0.00181 | 0.28 | 0.852 | 1.42e-07 | 3.56e-08
TUMOR STAGE | Chi-square test | 0.0119 | 0.633 | 0.00415 | 0.32 | 0.0429 | 0.0126 | 0.762 | 0.998 | 0.0189 | 0.0275
RADIATIONS RADIATION REGIMENINDICATION | Fisher's exact test | 0.393 | 0.496 | 0.216 | 0.0662 | 0.826 | 0.165 | 0.41 | 1 | 0.128 | 0.46
NEOADJUVANT THERAPY | Fisher's exact test | 0.127 | 0.712 | 0.645 | 0.279 | 0.735 | 0.216 | 0.41 | 1 | 4.93e-07 | 8.37e-05

Clustering Approach #1: 'mRNA CNMF subtypes'

Table S1. Get Full Table Description of clustering approach #1: 'mRNA CNMF subtypes'

Cluster Labels | 1 | 2 | 3 | 4
--- | --- | --- | --- | ---
Number of samples | 63 | 48 | 73 | 40

'mRNA CNMF subtypes' versus 'Time to Death'

P value = 0.145 (logrank test)

Table S2. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 114 | 15 | 0.9 - 52.0 (5.5)
subtype1 | 36 | 9 | 1.0 - 52.0 (13.0)
subtype2 | 26 | 2 | 1.0 - 30.0 (1.0)
subtype3 | 28 | 2 | 0.9 - 49.9 (1.0)
subtype4 | 24 | 2 | 0.9 - 52.0 (12.5)

Figure S1. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #1: 'Time to Death'

'mRNA CNMF subtypes' versus 'AGE'

P value = 0.596 (ANOVA)

Table S3. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 224 | 69.3 (11.5)
subtype1 | 63 | 67.7 (9.7)
subtype2 | 48 | 70.3 (11.8)
subtype3 | 73 | 69.6 (12.3)
subtype4 | 40 | 70.2 (12.2)

Figure S2. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #2: 'AGE'

'mRNA CNMF subtypes' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 0.0126 (Fisher's exact test)

Table S4. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | COLON | RECTUM
--- | --- | ---
ALL | 154 | 68
subtype1 | 37 | 26
subtype2 | 41 | 7
subtype3 | 46 | 25
subtype4 | 30 | 10

Figure S3. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'mRNA CNMF subtypes' versus 'GENDER'

P value = 0.072 (Fisher's exact test)

Table S5. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 107 | 117
subtype1 | 33 | 30
subtype2 | 29 | 19
subtype3 | 31 | 42
subtype4 | 14 | 26

Figure S4. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #4: 'GENDER'

'mRNA CNMF subtypes' versus 'HISTOLOGICAL.TYPE'

P value = 6.39e-07 (Chi-square test)

Table S6. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 128 | 24 | 58 | 7
subtype1 | 36 | 1 | 26 | 0
subtype2 | 27 | 13 | 4 | 2
subtype3 | 45 | 1 | 21 | 2
subtype4 | 20 | 9 | 7 | 3

Figure S5. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'mRNA CNMF subtypes' versus 'PATHOLOGY.T'

P value = 0.184 (Chi-square test)

Table S7. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 9 | 46 | 150 | 17
subtype1 | 1 | 12 | 42 | 8
subtype2 | 1 | 9 | 32 | 4
subtype3 | 5 | 16 | 52 | 0
subtype4 | 2 | 9 | 24 | 5

Figure S6. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY.T'

'mRNA CNMF subtypes' versus 'PATHOLOGY.N'

P value = 0.00595 (Chi-square test)

Table S8. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 137 | 43 | 44
subtype1 | 28 | 18 | 17
subtype2 | 30 | 6 | 12
subtype3 | 47 | 12 | 14
subtype4 | 32 | 7 | 1

Figure S7. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGY.N'

'mRNA CNMF subtypes' versus 'PATHOLOGICSPREAD(M)'

P value = 0.00173 (Chi-square test)

Table S9. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A
--- | --- | --- | ---
ALL | 186 | 34 | 1
subtype1 | 44 | 19 | 0
subtype2 | 41 | 6 | 0
subtype3 | 64 | 8 | 0
subtype4 | 37 | 1 | 1

Figure S8. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

'mRNA CNMF subtypes' versus 'TUMOR.STAGE'

P value = 0.0119 (Chi-square test)

Table S10. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 46 | 86 | 55 | 32
subtype1 | 9 | 16 | 19 | 17
subtype2 | 8 | 21 | 12 | 5
subtype3 | 19 | 28 | 18 | 8
subtype4 | 10 | 21 | 6 | 2

Figure S9. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #9: 'TUMOR.STAGE'

'mRNA CNMF subtypes' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.393 (Fisher's exact test)

Table S11. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 1 | 223
subtype1 | 0 | 63
subtype2 | 1 | 47
subtype3 | 0 | 73
subtype4 | 0 | 40

Figure S10. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'mRNA CNMF subtypes' versus 'NEOADJUVANT.THERAPY'

P value = 0.127 (Fisher's exact test)

Table S12. Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #11: 'NEOADJUVANT.THERAPY'

nPatients | NO | YES
--- | --- | ---
ALL | 8 | 216
subtype1 | 3 | 60
subtype2 | 4 | 44
subtype3 | 1 | 72
subtype4 | 0 | 40

Figure S11. Get High-res Image Clustering Approach #1: 'mRNA CNMF subtypes' versus Clinical Feature #11: 'NEOADJUVANT.THERAPY'

Clustering Approach #2: 'mRNA cHierClus subtypes'

Table S13. Get Full Table Description of clustering approach #2: 'mRNA cHierClus subtypes'

Cluster Labels | 1 | 2 | 3
--- | --- | --- | ---
Number of samples | 47 | 64 | 113

'mRNA cHierClus subtypes' versus 'Time to Death'

P value = 0.805 (logrank test)

Table S14. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 114 | 15 | 0.9 - 52.0 (5.5)
subtype1 | 12 | 1 | 0.9 - 17.0 (1.0)
subtype2 | 35 | 3 | 1.0 - 41.0 (1.0)
subtype3 | 67 | 11 | 0.9 - 52.0 (12.0)

Figure S12. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'

'mRNA cHierClus subtypes' versus 'AGE'

P value = 0.148 (ANOVA)

Table S15. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 224 | 69.3 (11.5)
subtype1 | 47 | 67.5 (13.0)
subtype2 | 64 | 71.6 (11.3)
subtype3 | 113 | 68.8 (10.8)

Figure S13. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #2: 'AGE'

'mRNA cHierClus subtypes' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 0.035 (Fisher's exact test)

Table S16. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | COLON | RECTUM
--- | --- | ---
ALL | 154 | 68
subtype1 | 34 | 12
subtype2 | 51 | 13
subtype3 | 69 | 43

Figure S14. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'mRNA cHierClus subtypes' versus 'GENDER'

P value = 0.796 (Fisher's exact test)

Table S17. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 107 | 117
subtype1 | 22 | 25
subtype2 | 33 | 31
subtype3 | 52 | 61

Figure S15. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #4: 'GENDER'

'mRNA cHierClus subtypes' versus 'HISTOLOGICAL.TYPE'

P value = 3.6e-08 (Chi-square test)

Table S18. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 128 | 24 | 58 | 7
subtype1 | 33 | 1 | 11 | 1
subtype2 | 29 | 20 | 9 | 3
subtype3 | 66 | 3 | 38 | 3

Figure S16. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'mRNA cHierClus subtypes' versus 'PATHOLOGY.T'

P value = 0.866 (Chi-square test)

Table S19. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 9 | 46 | 150 | 17
subtype1 | 1 | 9 | 35 | 2
subtype2 | 2 | 13 | 41 | 6
subtype3 | 6 | 24 | 74 | 9

Figure S17. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY.T'

'mRNA cHierClus subtypes' versus 'PATHOLOGY.N'

P value = 0.65 (Chi-square test)

Table S20. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 137 | 43 | 44
subtype1 | 28 | 11 | 8
subtype2 | 43 | 11 | 10
subtype3 | 66 | 21 | 26

Figure S18. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #7: 'PATHOLOGY.N'

'mRNA cHierClus subtypes' versus 'PATHOLOGICSPREAD(M)'

P value = 0.498 (Chi-square test)

Table S21. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A
--- | --- | --- | ---
ALL | 186 | 34 | 1
subtype1 | 38 | 8 | 0
subtype2 | 57 | 6 | 0
subtype3 | 91 | 20 | 1

Figure S19. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

'mRNA cHierClus subtypes' versus 'TUMOR.STAGE'

P value = 0.633 (Chi-square test)

Table S22. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 46 | 86 | 55 | 32
subtype1 | 9 | 19 | 11 | 8
subtype2 | 13 | 29 | 15 | 5
subtype3 | 24 | 38 | 29 | 19

Figure S20. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #9: 'TUMOR.STAGE'

'mRNA cHierClus subtypes' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.496 (Fisher's exact test)

Table S23. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 1 | 223
subtype1 | 0 | 47
subtype2 | 1 | 63
subtype3 | 0 | 113

Figure S21. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'mRNA cHierClus subtypes' versus 'NEOADJUVANT.THERAPY'

P value = 0.712 (Fisher's exact test)

Table S24. Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #11: 'NEOADJUVANT.THERAPY'

nPatients | NO | YES
--- | --- | ---
ALL | 8 | 216
subtype1 | 2 | 45
subtype2 | 3 | 61
subtype3 | 3 | 110

Figure S22. Get High-res Image Clustering Approach #2: 'mRNA cHierClus subtypes' versus Clinical Feature #11: 'NEOADJUVANT.THERAPY'

Clustering Approach #3: 'CN CNMF'

Table S25. Get Full Table Description of clustering approach #3: 'CN CNMF'

Cluster Labels | 1 | 2 | 3 | 4
--- | --- | --- | --- | ---
Number of samples | 200 | 234 | 100 | 41

'CN CNMF' versus 'Time to Death'

P value = 0.372 (logrank test)

Table S26. Clustering Approach #3: 'CN CNMF' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 444 | 60 | 0.1 - 135.5 (7.0)
subtype1 | 150 | 22 | 0.1 - 129.1 (8.0)
subtype2 | 191 | 22 | 0.1 - 135.5 (6.0)
subtype3 | 73 | 12 | 0.2 - 112.7 (6.6)
subtype4 | 30 | 4 | 0.3 - 87.8 (13.3)

Figure S23. Get High-res Image Clustering Approach #3: 'CN CNMF' versus Clinical Feature #1: 'Time to Death'

'CN CNMF' versus 'AGE'

P value = 0.628 (ANOVA)

Table S27. Clustering Approach #3: 'CN CNMF' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 574 | 66.6 (12.7)
subtype1 | 200 | 66.8 (11.2)
subtype2 | 233 | 66.8 (14.1)
subtype3 | 100 | 66.8 (12.1)
subtype4 | 41 | 64.1 (13.4)

Figure S24. Get High-res Image Clustering Approach #3: 'CN CNMF' versus Clinical Feature #2: 'AGE'

'CN CNMF' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 7.44e-05 (Fisher's exact test)

Table S28. Clustering Approach #3: 'CN CNMF' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | COLON | RECTUM
--- | --- | ---
ALL | 412 | 159
subtype1 | 124 | 72
subtype2 | 192 | 42
subtype3 | 66 | 34
subtype4 | 30 | 11

Figure S25. Get High-res Image Clustering Approach #3: 'CN CNMF' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'CN CNMF' versus 'GENDER'

P value = 0.804 (Fisher's exact test)

Table S29. Clustering Approach #3: 'CN CNMF' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 267 | 308
subtype1 | 88 | 112
subtype2 | 113 | 121
subtype3 | 48 | 52
subtype4 | 18 | 23

Figure S26. Get High-res Image Clustering Approach #3: 'CN CNMF' versus Clinical Feature #4: 'GENDER'

'CN CNMF' versus 'HISTOLOGICAL.TYPE'

P value = 4.28e-13 (Chi-square test)

Table S30. Clustering Approach #3: 'CN CNMF' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 356 | 54 | 143 | 13
subtype1 | 121 | 3 | 72 | 0
subtype2 | 144 | 46 | 32 | 9
subtype3 | 61 | 5 | 28 | 4
subtype4 | 30 | 0 | 11 | 0

Figure S27. Get High-res Image Clustering Approach #3: 'CN CNMF' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'CN CNMF' versus 'PATHOLOGY.T'

P value = 0.934 (Chi-square test)

Table S31. Clustering Approach #3: 'CN CNMF' versus Clinical Feature #6: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 20 | 101 | 392 | 59
subtype1 | 7 | 31 | 140 | 22
subtype2 | 10 | 44 | 154 | 24
subtype3 | 2 | 18 | 69 | 11
subtype4 | 1 | 8 | 29 | 2

Figure S28. Get High-res Image Clustering Approach #3: 'CN CNMF' versus Clinical Feature #6: 'PATHOLOGY.T'

'CN CNMF' versus 'PATHOLOGY.N'

P value = 0.00155 (Chi-square test)

Table S32. Clustering Approach #3: 'CN CNMF' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 328 | 140 | 103
subtype1 | 96 | 64 | 38
subtype2 | 157 | 45 | 32
subtype3 | 51 | 22 | 26
subtype4 | 24 | 9 | 7

Figure S29. Get High-res Image Clustering Approach #3: 'CN CNMF' versus Clinical Feature #7: 'PATHOLOGY.N'

'CN CNMF' versus 'PATHOLOGICSPREAD(M)'

P value = 0.2 (Chi-square test)

Table S33. Clustering Approach #3: 'CN CNMF' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 435 | 71 | 9 | 1 | 49
subtype1 | 143 | 35 | 4 | 0 | 16
subtype2 | 189 | 16 | 2 | 1 | 21
subtype3 | 72 | 15 | 2 | 0 | 10
subtype4 | 31 | 5 | 1 | 0 | 2

Figure S30. Get High-res Image Clustering Approach #3: 'CN CNMF' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

'CN CNMF' versus 'TUMOR.STAGE'

P value = 0.00415 (Chi-square test)

Table S34. Clustering Approach #3: 'CN CNMF' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 97 | 207 | 166 | 81
subtype1 | 28 | 58 | 68 | 38
subtype2 | 47 | 100 | 58 | 19
subtype3 | 16 | 32 | 32 | 18
subtype4 | 6 | 17 | 8 | 6

Figure S31. Get High-res Image Clustering Approach #3: 'CN CNMF' versus Clinical Feature #9: 'TUMOR.STAGE'

'CN CNMF' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.216 (Fisher's exact test)

Table S35. Clustering Approach #3: 'CN CNMF' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 9 | 566
subtype1 | 3 | 197
subtype2 | 2 | 232
subtype3 | 2 | 98
subtype4 | 2 | 39

Figure S32. Get High-res Image Clustering Approach #3: 'CN CNMF' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'CN CNMF' versus 'NEOADJUVANT.THERAPY'

P value = 0.645 (Fisher's exact test)

Table S36. Clustering Approach #3: 'CN CNMF' versus Clinical Feature #11: 'NEOADJUVANT.THERAPY'

nPatients | NO | YES
--- | --- | ---
ALL | 82 | 493
subtype1 | 25 | 175
subtype2 | 35 | 199
subtype3 | 14 | 86
subtype4 | 8 | 33

Figure S33. Get High-res Image Clustering Approach #3: 'CN CNMF' versus Clinical Feature #11: 'NEOADJUVANT.THERAPY'

Clustering Approach #4: 'METHLYATION CNMF'

Table S37. Get Full Table Description of clustering approach #4: 'METHLYATION CNMF'

Cluster Labels | 1 | 2 | 3
--- | --- | --- | ---
Number of samples | 141 | 111 | 97

'METHLYATION CNMF' versus 'Time to Death'

P value = 0.918 (logrank test)

Table S38. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 324 | 44 | 0.1 - 135.5 (7.0)
subtype1 | 131 | 18 | 0.1 - 135.5 (7.1)
subtype2 | 102 | 16 | 0.1 - 129.1 (7.5)
subtype3 | 91 | 10 | 0.1 - 102.4 (6.0)

Figure S34. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #1: 'Time to Death'

'METHLYATION CNMF' versus 'AGE'

P value = 0.00372 (ANOVA)

Table S39. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 348 | 64.8 (13.0)
subtype1 | 141 | 65.0 (12.6)
subtype2 | 111 | 67.5 (12.9)
subtype3 | 96 | 61.5 (13.1)

Figure S35. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #2: 'AGE'

'METHLYATION CNMF' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 0.00624 (Fisher's exact test)

Table S40. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | COLON | RECTUM
--- | --- | ---
ALL | 254 | 93
subtype1 | 94 | 47
subtype2 | 93 | 18
subtype3 | 67 | 28

Figure S36. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'METHLYATION CNMF' versus 'GENDER'

P value = 0.031 (Fisher's exact test)

Table S41. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 156 | 193
subtype1 | 61 | 80
subtype2 | 60 | 51
subtype3 | 35 | 62

Figure S37. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #4: 'GENDER'

'METHLYATION CNMF' versus 'HISTOLOGICAL.TYPE'

P value = 0.00456 (Chi-square test)

Table S42. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 224 | 30 | 87 | 6
subtype1 | 89 | 5 | 45 | 2
subtype2 | 80 | 13 | 15 | 3
subtype3 | 55 | 12 | 27 | 1

Figure S38. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'METHLYATION CNMF' versus 'PATHOLOGY.T'

P value = 0.569 (Chi-square test)

Table S43. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #6: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 11 | 51 | 243 | 42
subtype1 | 4 | 21 | 100 | 16
subtype2 | 4 | 20 | 76 | 10
subtype3 | 3 | 10 | 67 | 16

Figure S39. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #6: 'PATHOLOGY.T'

'METHLYATION CNMF' versus 'PATHOLOGY.N'

P value = 0.429 (Chi-square test)

Table S44. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 193 | 93 | 58
subtype1 | 71 | 43 | 23
subtype2 | 69 | 23 | 19
subtype3 | 53 | 27 | 16

Figure S40. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #7: 'PATHOLOGY.N'

'METHLYATION CNMF' versus 'PATHOLOGICSPREAD(M)'

P value = 0.686 (Chi-square test)

Table S45. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 246 | 37 | 8 | 1 | 50
subtype1 | 96 | 19 | 4 | 0 | 21
subtype2 | 80 | 10 | 1 | 1 | 16
subtype3 | 70 | 8 | 3 | 0 | 13

Figure S41. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

'METHLYATION CNMF' versus 'TUMOR.STAGE'

P value = 0.32 (Chi-square test)

Table S46. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 48 | 126 | 106 | 49
subtype1 | 16 | 46 | 49 | 23
subtype2 | 21 | 44 | 27 | 14
subtype3 | 11 | 36 | 30 | 12

Figure S42. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #9: 'TUMOR.STAGE'

'METHLYATION CNMF' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.0662 (Fisher's exact test)

Table S47. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 8 | 341
subtype1 | 4 | 137
subtype2 | 0 | 111
subtype3 | 4 | 93

Figure S43. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'METHLYATION CNMF' versus 'NEOADJUVANT.THERAPY'

P value = 0.279 (Fisher's exact test)

Table S48. Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #11: 'NEOADJUVANT.THERAPY'

nPatients | NO | YES
--- | --- | ---
ALL | 74 | 275
subtype1 | 28 | 113
subtype2 | 20 | 91
subtype3 | 26 | 71

Figure S44. Get High-res Image Clustering Approach #4: 'METHLYATION CNMF' versus Clinical Feature #11: 'NEOADJUVANT.THERAPY'

Clustering Approach #5: 'RPPA CNMF subtypes'

Table S49. Get Full Table Description of clustering approach #5: 'RPPA CNMF subtypes'

Cluster Labels | 1 | 2 | 3 | 4
--- | --- | --- | --- | ---
Number of samples | 96 | 160 | 20 | 123

'RPPA CNMF subtypes' versus 'Time to Death'

P value = 0.273 (logrank test)

Table S50. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 308 | 30 | 0.1 - 121.1 (6.0)
subtype1 | 70 | 4 | 0.1 - 87.8 (4.4)
subtype2 | 117 | 13 | 0.1 - 121.1 (6.0)
subtype3 | 13 | 0 | 0.2 - 41.0 (7.6)
subtype4 | 108 | 13 | 0.1 - 105.3 (7.0)

Figure S45. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #1: 'Time to Death'

'RPPA CNMF subtypes' versus 'AGE'

P value = 0.467 (ANOVA)

Table S51. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 398 | 66.2 (12.8)
subtype1 | 96 | 66.6 (12.0)
subtype2 | 159 | 66.1 (12.9)
subtype3 | 20 | 70.3 (10.0)
subtype4 | 123 | 65.5 (13.8)

Figure S46. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #2: 'AGE'

'RPPA CNMF subtypes' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 0.469 (Fisher's exact test)

Table S52. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | COLON | RECTUM
--- | --- | ---
ALL | 269 | 130
subtype1 | 64 | 32
subtype2 | 106 | 54
subtype3 | 11 | 9
subtype4 | 88 | 35

Figure S47. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'RPPA CNMF subtypes' versus 'GENDER'

P value = 0.474 (Fisher's exact test)

Table S53. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 187 | 212
subtype1 | 39 | 57
subtype2 | 81 | 79
subtype3 | 10 | 10
subtype4 | 57 | 66

Figure S48. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #4: 'GENDER'

'RPPA CNMF subtypes' versus 'HISTOLOGICAL.TYPE'

P value = 0.447 (Chi-square test)

Table S54. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 238 | 30 | 117 | 10
subtype1 | 54 | 10 | 26 | 4
subtype2 | 99 | 7 | 49 | 4
subtype3 | 9 | 2 | 8 | 1
subtype4 | 76 | 11 | 34 | 1

Figure S49. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'RPPA CNMF subtypes' versus 'PATHOLOGY.T'

P value = 0.455 (Chi-square test)

Table S55. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 10 | 68 | 276 | 41
subtype1 | 0 | 14 | 68 | 13
subtype2 | 5 | 26 | 110 | 16
subtype3 | 0 | 4 | 16 | 0
subtype4 | 5 | 24 | 82 | 12

Figure S50. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY.T'

'RPPA CNMF subtypes' versus 'PATHOLOGY.N'

P value = 0.0253 (Chi-square test)

Table S56. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 224 | 103 | 68
subtype1 | 45 | 29 | 20
subtype2 | 82 | 47 | 31
subtype3 | 15 | 2 | 2
subtype4 | 82 | 25 | 15

Figure S51. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGY.N'

'RPPA CNMF subtypes' versus 'PATHOLOGICSPREAD(M)'

P value = 0.0189 (Chi-square test)

Table S57. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 300 | 49 | 8 | 1 | 36
subtype1 | 72 | 12 | 5 | 0 | 5
subtype2 | 111 | 29 | 0 | 1 | 17
subtype3 | 18 | 1 | 0 | 0 | 1
subtype4 | 99 | 7 | 3 | 0 | 13

Figure S52. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

'RPPA CNMF subtypes' versus 'TUMOR.STAGE'

P value = 0.0429 (Chi-square test)

Table S58. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 61 | 147 | 119 | 57
subtype1 | 11 | 31 | 32 | 16
subtype2 | 23 | 50 | 51 | 30
subtype3 | 4 | 11 | 3 | 1
subtype4 | 23 | 55 | 33 | 10

Figure S53. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #9: 'TUMOR.STAGE'

'RPPA CNMF subtypes' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.826 (Fisher's exact test)

Table S59. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 8 | 391
subtype1 | 3 | 93
subtype2 | 3 | 157
subtype3 | 0 | 20
subtype4 | 2 | 121

Figure S54. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'RPPA CNMF subtypes' versus 'NEOADJUVANT.THERAPY'

P value = 0.735 (Fisher's exact test)

Table S60. Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #11: 'NEOADJUVANT.THERAPY'

nPatients | NO | YES
--- | --- | ---
ALL | 68 | 331
subtype1 | 20 | 76
subtype2 | 25 | 135
subtype3 | 3 | 17
subtype4 | 20 | 103

Figure S55. Get High-res Image Clustering Approach #5: 'RPPA CNMF subtypes' versus Clinical Feature #11: 'NEOADJUVANT.THERAPY'

Clustering Approach #6: 'RPPA cHierClus subtypes'

Table S61. Get Full Table Description of clustering approach #6: 'RPPA cHierClus subtypes'

Cluster Labels | 1 | 2 | 3 | 4
--- | --- | --- | --- | ---
Number of samples | 210 | 34 | 72 | 83

'RPPA cHierClus subtypes' versus 'Time to Death'

P value = 0.0945 (logrank test)

Table S62. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 308 | 30 | 0.1 - 121.1 (6.0)
subtype1 | 148 | 15 | 0.1 - 121.1 (5.9)
subtype2 | 22 | 3 | 0.1 - 105.3 (8.1)
subtype3 | 65 | 2 | 0.1 - 87.8 (5.4)
subtype4 | 73 | 10 | 0.1 - 100.0 (6.1)

Figure S56. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'

'RPPA cHierClus subtypes' versus 'AGE'

P value = 0.505 (ANOVA)

Table S63. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 398 | 66.2 (12.8)
subtype1 | 209 | 66.8 (13.2)
subtype2 | 34 | 67.9 (11.8)
subtype3 | 72 | 65.1 (12.1)
subtype4 | 83 | 65.1 (12.8)

Figure S57. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #2: 'AGE'

'RPPA cHierClus subtypes' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 0.258 (Fisher's exact test)

Table S64. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | COLON | RECTUM
--- | --- | ---
ALL | 269 | 130
subtype1 | 138 | 72
subtype2 | 28 | 6
subtype3 | 49 | 23
subtype4 | 54 | 29

Figure S58. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'RPPA cHierClus subtypes' versus 'GENDER'

P value = 0.121 (Fisher's exact test)

Table S65. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 187 | 212
subtype1 | 105 | 105
subtype2 | 19 | 15
subtype3 | 33 | 39
subtype4 | 30 | 53

Figure S59. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #4: 'GENDER'

'RPPA cHierClus subtypes' versus 'HISTOLOGICAL.TYPE'

P value = 0.272 (Chi-square test)

Table S66. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 238 | 30 | 117 | 10
subtype1 | 125 | 12 | 63 | 6
subtype2 | 25 | 3 | 5 | 1
subtype3 | 40 | 9 | 20 | 3
subtype4 | 48 | 6 | 29 | 0

Figure S60. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'RPPA cHierClus subtypes' versus 'PATHOLOGY.T'

P value = 0.527 (Chi-square test)

Table S67. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 10 | 68 | 276 | 41
subtype1 | 5 | 35 | 145 | 22
subtype2 | 1 | 3 | 28 | 2
subtype3 | 1 | 11 | 48 | 11
subtype4 | 3 | 19 | 55 | 6

Figure S61. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY.T'

'RPPA cHierClus subtypes' versus 'PATHOLOGY.N'

P value = 0.0289 (Chi-square test)

Table S68. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 224 | 103 | 68
subtype1 | 107 | 62 | 40
subtype2 | 22 | 7 | 5
subtype3 | 35 | 20 | 15
subtype4 | 60 | 14 | 8

Figure S62. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #7: 'PATHOLOGY.N'

'RPPA cHierClus subtypes' versus 'PATHOLOGICSPREAD(M)'

P value = 0.00181 (Chi-square test)

Table S69. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 300 | 49 | 8 | 1 | 36
subtype1 | 153 | 37 | 0 | 1 | 19
subtype2 | 29 | 0 | 0 | 0 | 3
subtype3 | 53 | 8 | 5 | 0 | 4
subtype4 | 65 | 4 | 3 | 0 | 10

Figure S63. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

'RPPA cHierClus subtypes' versus 'TUMOR.STAGE'

P value = 0.0126 (Chi-square test)

Table S70. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 61 | 147 | 119 | 57
subtype1 | 31 | 69 | 65 | 37
subtype2 | 3 | 18 | 12 | 0
subtype3 | 9 | 22 | 24 | 13
subtype4 | 18 | 38 | 18 | 7

Figure S64. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #9: 'TUMOR.STAGE'

'RPPA cHierClus subtypes' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.165 (Fisher's exact test)

Table S71. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 8 | 391
subtype1 | 3 | 207
subtype2 | 0 | 34
subtype3 | 4 | 68
subtype4 | 1 | 82

Figure S65. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'RPPA cHierClus subtypes' versus 'NEOADJUVANT.THERAPY'

P value = 0.216 (Fisher's exact test)

Table S72. Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #11: 'NEOADJUVANT.THERAPY'

nPatients | NO | YES
--- | --- | ---
ALL | 68 | 331
subtype1 | 31 | 179
subtype2 | 8 | 26
subtype3 | 17 | 55
subtype4 | 12 | 71

Figure S66. Get High-res Image Clustering Approach #6: 'RPPA cHierClus subtypes' versus Clinical Feature #11: 'NEOADJUVANT.THERAPY'

Clustering Approach #7: 'RNAseq CNMF subtypes'

Table S73. Get Full Table Description of clustering approach #7: 'RNAseq CNMF subtypes'

Cluster Labels | 1 | 2 | 3 | 4
--- | --- | --- | --- | ---
Number of samples | 17 | 17 | 27 | 22

'RNAseq CNMF subtypes' versus 'Time to Death'

P value = 0.12 (logrank test)

Table S74. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 46 | 4 | 0.9 - 72.1 (8.2)
subtype1 | 6 | 1 | 1.0 - 64.0 (11.6)
subtype2 | 8 | 0 | 1.0 - 17.0 (1.0)
subtype3 | 16 | 0 | 0.9 - 61.9 (8.5)
subtype4 | 16 | 3 | 0.9 - 72.1 (7.0)

Figure S67. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #1: 'Time to Death'

'RNAseq CNMF subtypes' versus 'AGE'

P value = 0.416 (ANOVA)

Table S75. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 83 | 67.6 (10.5)
subtype1 | 17 | 64.8 (9.6)
subtype2 | 17 | 66.1 (9.8)
subtype3 | 27 | 68.2 (12.3)
subtype4 | 22 | 70.1 (9.3)

Figure S68. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #2: 'AGE'

'RNAseq CNMF subtypes' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 0.111 (Fisher's exact test)

Table S76. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | COLON | RECTUM
--- | --- | ---
ALL | 11 | 71
subtype1 | 3 | 14
subtype2 | 3 | 13
subtype3 | 5 | 22
subtype4 | 0 | 22

Figure S69. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'RNAseq CNMF subtypes' versus 'GENDER'

P value = 0.869 (Fisher's exact test)

Table S77. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 39 | 44
subtype1 | 9 | 8
subtype2 | 8 | 9
subtype3 | 11 | 16
subtype4 | 11 | 11

Figure S70. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #4: 'GENDER'

'RNAseq CNMF subtypes' versus 'HISTOLOGICAL.TYPE'

P value = 0.0132 (Chi-square test)

Table S78. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | ---
ALL | 11 | 60 | 8
subtype1 | 3 | 11 | 2
subtype2 | 3 | 13 | 0
subtype3 | 5 | 14 | 6
subtype4 | 0 | 22 | 0

Figure S71. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'RNAseq CNMF subtypes' versus 'PATHOLOGY.T'

P value = 0.439 (Chi-square test)

Table S79. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 5 | 19 | 54 | 5
subtype1 | 0 | 2 | 14 | 1
subtype2 | 1 | 4 | 12 | 0
subtype3 | 3 | 6 | 17 | 1
subtype4 | 1 | 7 | 11 | 3

Figure S72. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY.T'

'RNAseq CNMF subtypes' versus 'PATHOLOGY.N'

P value = 0.872 (Chi-square test)

Table S80. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 52 | 17 | 14
subtype1 | 9 | 4 | 4
subtype2 | 12 | 3 | 2
subtype3 | 18 | 6 | 3
subtype4 | 13 | 4 | 5

Figure S73. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGY.N'

'RNAseq CNMF subtypes' versus 'PATHOLOGICSPREAD(M)'

P value = 0.28 (Chi-square test)

Table S81. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A
--- | --- | --- | ---
ALL | 68 | 13 | 1
subtype1 | 13 | 4 | 0
subtype2 | 16 | 1 | 0
subtype3 | 23 | 2 | 1
subtype4 | 16 | 6 | 0

Figure S74. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

'RNAseq CNMF subtypes' versus 'TUMOR.STAGE'

P value = 0.762 (Chi-square test)

Table S82. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 21 | 29 | 18 | 13
subtype1 | 2 | 7 | 4 | 3
subtype2 | 5 | 7 | 4 | 1
subtype3 | 8 | 9 | 6 | 3
subtype4 | 6 | 6 | 4 | 6

Figure S75. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #9: 'TUMOR.STAGE'

'RNAseq CNMF subtypes' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.41 (Fisher's exact test)

Table S83. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 1 | 82
subtype1 | 1 | 16
subtype2 | 0 | 17
subtype3 | 0 | 27
subtype4 | 0 | 22

Figure S76. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'RNAseq CNMF subtypes' versus 'NEOADJUVANT.THERAPY'

P value = 0.41 (Fisher's exact test)

Table S84. Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #11: 'NEOADJUVANT.THERAPY'

nPatients | NO | YES
--- | --- | ---
ALL | 1 | 82
subtype1 | 1 | 16
subtype2 | 0 | 17
subtype3 | 0 | 27
subtype4 | 0 | 22

Figure S77. Get High-res Image Clustering Approach #7: 'RNAseq CNMF subtypes' versus Clinical Feature #11: 'NEOADJUVANT.THERAPY'

Clustering Approach #8: 'RNAseq cHierClus subtypes'

Table S85. Get Full Table Description of clustering approach #8: 'RNAseq cHierClus subtypes'

Cluster Labels | 1 | 2 | 3 | 4
--- | --- | --- | --- | ---
Number of samples | 17 | 16 | 28 | 22

'RNAseq cHierClus subtypes' versus 'Time to Death'

P value = 0.176 (logrank test)

Table S86. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 46 | 4 | 0.9 - 72.1 (8.2)
subtype1 | 9 | 1 | 0.9 - 38.9 (2.0)
subtype2 | 11 | 1 | 1.0 - 52.0 (12.0)
subtype3 | 14 | 0 | 0.9 - 61.9 (8.5)
subtype4 | 12 | 2 | 1.0 - 72.1 (1.5)

Figure S78. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'

'RNAseq cHierClus subtypes' versus 'AGE'

P value = 0.884 (ANOVA)

Table S87. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 83 | 67.6 (10.5)
subtype1 | 17 | 69.2 (9.1)
subtype2 | 16 | 66.5 (9.4)
subtype3 | 28 | 67.7 (13.0)
subtype4 | 22 | 67.0 (9.2)

Figure S79. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #2: 'AGE'

'RNAseq cHierClus subtypes' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 0.265 (Fisher's exact test)

Table S88. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | COLON | RECTUM
--- | --- | ---
ALL | 11 | 71
subtype1 | 1 | 15
subtype2 | 1 | 15
subtype3 | 7 | 21
subtype4 | 2 | 20

Figure S80. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'RNAseq cHierClus subtypes' versus 'GENDER'

P value = 0.924 (Fisher's exact test)

Table S89. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 39 | 44
subtype1 | 8 | 9
subtype2 | 8 | 8
subtype3 | 14 | 14
subtype4 | 9 | 13

Figure S81. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #4: 'GENDER'

'RNAseq cHierClus subtypes' versus 'HISTOLOGICAL.TYPE'

P value = 0.00215 (Chi-square test)

Table S90. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | ---
ALL | 11 | 60 | 8
subtype1 | 1 | 13 | 1
subtype2 | 1 | 15 | 0
subtype3 | 7 | 12 | 7
subtype4 | 2 | 20 | 0

Figure S82. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'RNAseq cHierClus subtypes' versus 'PATHOLOGY.T'

P value = 0.71 (Chi-square test)

Table S91. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 5 | 19 | 54 | 5
subtype1 | 1 | 4 | 12 | 0
subtype2 | 2 | 4 | 9 | 1
subtype3 | 2 | 6 | 19 | 1
subtype4 | 0 | 5 | 14 | 3

Figure S83. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY.T'

'RNAseq cHierClus subtypes' versus 'PATHOLOGY.N'

P value = 0.969 (Chi-square test)

Table S92. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 52 | 17 | 14
subtype1 | 10 | 4 | 3
subtype2 | 10 | 4 | 2
subtype3 | 19 | 5 | 4
subtype4 | 13 | 4 | 5

Figure S84. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #7: 'PATHOLOGY.N'

'RNAseq cHierClus subtypes' versus 'PATHOLOGICSPREAD(M)'

P value = 0.852 (Chi-square test)

Table S93. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A
--- | --- | --- | ---
ALL | 68 | 13 | 1
subtype1 | 14 | 3 | 0
subtype2 | 13 | 3 | 0
subtype3 | 23 | 3 | 1
subtype4 | 18 | 4 | 0

Figure S85. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

'RNAseq cHierClus subtypes' versus 'TUMOR.STAGE'

P value = 0.998 (Chi-square test)

Table S94. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 21 | 29 | 18 | 13
subtype1 | 4 | 6 | 4 | 3
subtype2 | 5 | 4 | 4 | 3
subtype3 | 7 | 11 | 5 | 4
subtype4 | 5 | 8 | 5 | 3

Figure S86. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #9: 'TUMOR.STAGE'

'RNAseq cHierClus subtypes' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1 (Fisher's exact test)

Table S95. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 1 | 82
subtype1 | 0 | 17
subtype2 | 0 | 16
subtype3 | 1 | 27
subtype4 | 0 | 22

Figure S87. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'RNAseq cHierClus subtypes' versus 'NEOADJUVANT.THERAPY'

P value = 1 (Fisher's exact test)

Table S96. Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #11: 'NEOADJUVANT.THERAPY'

nPatients | NO | YES
--- | --- | ---
ALL | 1 | 82
subtype1 | 0 | 17
subtype2 | 0 | 16
subtype3 | 1 | 27
subtype4 | 0 | 22

Figure S88. Get High-res Image Clustering Approach #8: 'RNAseq cHierClus subtypes' versus Clinical Feature #11: 'NEOADJUVANT.THERAPY'

Clustering Approach #9: 'MIRseq CNMF subtypes'

Table S97. Get Full Table Description of clustering approach #9: 'MIRseq CNMF subtypes'

Cluster Labels | 1 | 2 | 3
--- | --- | --- | ---
Number of samples | 205 | 73 | 243

'MIRseq CNMF subtypes' versus 'Time to Death'

P value = 0.238 (logrank test)

Table S98. Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 386 | 59 | 0.1 - 135.5 (8.0)
subtype1 | 191 | 31 | 0.1 - 135.5 (8.1)
subtype2 | 65 | 10 | 0.1 - 100.0 (7.0)
subtype3 | 130 | 18 | 0.2 - 72.1 (6.5)

Figure S89. Get High-res Image Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #1: 'Time to Death'

'MIRseq CNMF subtypes' versus 'AGE'

P value = 0.00171 (ANOVA)

Table S99. Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 521 | 66.8 (12.7)
subtype1 | 205 | 65.8 (12.7)
subtype2 | 73 | 63.2 (13.6)
subtype3 | 243 | 68.7 (12.1)

Figure S90. Get High-res Image Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #2: 'AGE'

'MIRseq CNMF subtypes' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 0.565 (Fisher's exact test)

Table S100. Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | COLON | RECTUM
--- | --- | ---
ALL | 377 | 140
subtype1 | 145 | 59
subtype2 | 56 | 16
subtype3 | 176 | 65

Figure S91. Get High-res Image Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'MIRseq CNMF subtypes' versus 'GENDER'

P value = 0.471 (Fisher's exact test)

Table S101. Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 249 | 272
subtype1 | 99 | 106
subtype2 | 30 | 43
subtype3 | 120 | 123

Figure S92. Get High-res Image Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #4: 'GENDER'

'MIRseq CNMF subtypes' versus 'HISTOLOGICAL.TYPE'

P value = 0.0981 (Chi-square test)

Table S102. Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 327 | 48 | 127 | 10
subtype1 | 132 | 13 | 58 | 1
subtype2 | 45 | 11 | 14 | 2
subtype3 | 150 | 24 | 55 | 7

Figure S93. Get High-res Image Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'MIRseq CNMF subtypes' versus 'PATHOLOGY.T'

P value = 0.0706 (Chi-square test)

Table S103. Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 19 | 90 | 361 | 47
subtype1 | 8 | 35 | 145 | 16
subtype2 | 1 | 5 | 55 | 11
subtype3 | 10 | 50 | 161 | 20

Figure S94. Get High-res Image Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY.T'

'MIRseq CNMF subtypes' versus 'PATHOLOGY.N'

P value = 0.0069 (Chi-square test)

Table S104. Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 296 | 127 | 94
subtype1 | 117 | 58 | 29
subtype2 | 29 | 22 | 19
subtype3 | 150 | 47 | 46

Figure S95. Get High-res Image Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGY.N'

'MIRseq CNMF subtypes' versus 'PATHOLOGICSPREAD(M)'

P value = 1.42e-07 (Chi-square test)

Table S105. Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 393 | 67 | 9 | 1 | 42
subtype1 | 146 | 17 | 6 | 1 | 31
subtype2 | 49 | 11 | 2 | 0 | 10
subtype3 | 198 | 39 | 1 | 0 | 1

Figure S96. Get High-res Image Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

'MIRseq CNMF subtypes' versus 'TUMOR.STAGE'

P value = 0.0189 (Chi-square test)

Table S106. Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 90 | 188 | 149 | 75
subtype1 | 37 | 74 | 65 | 26
subtype2 | 3 | 23 | 27 | 12
subtype3 | 50 | 91 | 57 | 37

Figure S97. Get High-res Image Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #9: 'TUMOR.STAGE'

'MIRseq CNMF subtypes' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.128 (Fisher's exact test)

Table S107. Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 8 | 513
subtype1 | 3 | 202
subtype2 | 3 | 70
subtype3 | 2 | 241

Figure S98. Get High-res Image Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'MIRseq CNMF subtypes' versus 'NEOADJUVANT.THERAPY'

P value = 4.93e-07 (Fisher's exact test)

Table S108. Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #11: 'NEOADJUVANT.THERAPY'

nPatients | NO | YES
--- | --- | ---
ALL | 71 | 450
subtype1 | 43 | 162
subtype2 | 15 | 58
subtype3 | 13 | 230

Figure S99. Get High-res Image Clustering Approach #9: 'MIRseq CNMF subtypes' versus Clinical Feature #11: 'NEOADJUVANT.THERAPY'

Clustering Approach #10: 'MIRseq cHierClus subtypes'

Table S109. Get Full Table Description of clustering approach #10: 'MIRseq cHierClus subtypes'

Cluster Labels | 1 | 2 | 3
--- | --- | --- | ---
Number of samples | 45 | 220 | 256

'MIRseq cHierClus subtypes' versus 'Time to Death'

P value = 0.598 (logrank test)

Table S110. Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 386 | 59 | 0.1 - 135.5 (8.0)
subtype1 | 32 | 4 | 0.1 - 129.1 (4.5)
subtype2 | 120 | 17 | 0.9 - 72.1 (10.5)
subtype3 | 234 | 38 | 0.1 - 135.5 (8.0)

Figure S100. Get High-res Image Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'

'MIRseq cHierClus subtypes' versus 'AGE'

P value = 0.00388 (ANOVA)

Table S111. Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 521 | 66.8 (12.7)
subtype1 | 45 | 64.1 (13.2)
subtype2 | 220 | 68.9 (12.2)
subtype3 | 256 | 65.5 (12.8)

Figure S101. Get High-res Image Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #2: 'AGE'

'MIRseq cHierClus subtypes' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 0.0614 (Fisher's exact test)

Table S112. Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | COLON | RECTUM
--- | --- | ---
ALL | 377 | 140
subtype1 | 26 | 19
subtype2 | 164 | 54
subtype3 | 187 | 67

Figure S102. Get High-res Image Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'MIRseq cHierClus subtypes' versus 'GENDER'

P value = 0.683 (Fisher's exact test)

Table S113. Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 249 | 272
subtype1 | 24 | 21
subtype2 | 106 | 114
subtype3 | 119 | 137

Figure S103. Get High-res Image Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #4: 'GENDER'

'MIRseq cHierClus subtypes' versus 'HISTOLOGICAL.TYPE'

P value = 0.0326 (Chi-square test)

Table S114. Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 327 | 48 | 127 | 10
subtype1 | 24 | 2 | 16 | 3
subtype2 | 137 | 25 | 46 | 5
subtype3 | 166 | 21 | 65 | 2

Figure S104. Get High-res Image Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'MIRseq cHierClus subtypes' versus 'PATHOLOGY.T'

P value = 0.15 (Chi-square test)

Table S115. Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 19 | 90 | 361 | 47
subtype1 | 1 | 5 | 38 | 1
subtype2 | 9 | 47 | 143 | 19
subtype3 | 9 | 38 | 180 | 27

Figure S105. Get High-res Image Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY.T'

'MIRseq cHierClus subtypes' versus 'PATHOLOGY.N'

P value = 0.199 (Chi-square test)

Table S116. Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 296 | 127 | 94
subtype1 | 18 | 14 | 12
subtype2 | 132 | 49 | 38
subtype3 | 146 | 64 | 44

Figure S106. Get High-res Image Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #7: 'PATHOLOGY.N'

'MIRseq cHierClus subtypes' versus 'PATHOLOGICSPREAD(M)'

P value = 3.56e-08 (Chi-square test)

Table S117. Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 393 | 67 | 9 | 1 | 42
subtype1 | 29 | 12 | 1 | 0 | 3
subtype2 | 181 | 33 | 2 | 0 | 0
subtype3 | 183 | 22 | 6 | 1 | 39

Figure S107. Get High-res Image Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

'MIRseq cHierClus subtypes' versus 'TUMOR.STAGE'

P value = 0.0275 (Chi-square test)

Table S118. Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 90 | 188 | 149 | 75
subtype1 | 5 | 11 | 15 | 13
subtype2 | 46 | 77 | 56 | 30
subtype3 | 39 | 100 | 78 | 32

Figure S108. Get High-res Image Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #9: 'TUMOR.STAGE'

'MIRseq cHierClus subtypes' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.46 (Fisher's exact test)

Table S119. Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 8 | 513
subtype1 | 1 | 44
subtype2 | 2 | 218
subtype3 | 5 | 251

Figure S109. Get High-res Image Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'MIRseq cHierClus subtypes' versus 'NEOADJUVANT.THERAPY'

P value = 8.37e-05 (Fisher's exact test)

Table S120. Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #11: 'NEOADJUVANT.THERAPY'

nPatients | NO | YES
--- | --- | ---
ALL | 71 | 450
subtype1 | 8 | 37
subtype2 | 14 | 206
subtype3 | 49 | 207

Figure S110. Get High-res Image Clustering Approach #10: 'MIRseq cHierClus subtypes' versus Clinical Feature #11: 'NEOADJUVANT.THERAPY'

Methods & Data
Input

- Cluster data file = COADREAD.mergedcluster.txt

- Clinical data file = COADREAD.clin.merged.picked.txt

- Number of patients = 588

- Number of clustering approaches = 10

- Number of selected clinical features = 11

- Exclude small clusters that include fewer than K patients, K = 3

Clustering approaches
CNMF clustering

consensus non-negative matrix factorization clustering approach (Brunet et al. 2004)

Consensus hierarchical clustering

Resampling-based clustering method (Monti et al. 2003)

Survival analysis

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

ANOVA analysis

For continuous numerical clinical features, one-way analysis of variance (Howell 2002) was applied to compare the clinical values between tumor subtypes using 'anova' function in R

Fisher's exact test

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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Brunet et al., Metagenes and molecular pattern discovery using matrix factorization, PNAS 101(12):4164-9 (2004)
[2] Monti et al., Consensus Clustering: A Resampling-Based Method for Class Discovery and Visualization of Gene Expression Microarray Data, Machine Learning 52(1):91-118 (2003)
[3] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[4] Howell, D, Statistical Methods for Psychology. (5th ed.), Duxbury Press:324-5 (2002)
[5] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[6] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
Copyright © 2012 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle