Stomach 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 5 different clustering approaches and 9 clinical features across 136 patients, 4 significant findings detected with P value < 0.05.

- 3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.

- CNMF clustering analysis on sequencing-based mRNA expression data identified 6 subtypes that do not correlate to any clinical features.

- Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that do not correlate to any clinical features.

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

- Consensus hierarchical clustering analysis on sequencing-based miR expression data identified 3 subtypes that correlate to 'HISTOLOGICAL.TYPE'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between subtypes identified by 5 different clustering approaches and 9 clinical features. Shown in the table are P values from statistical tests. Thresholded by P value < 0.05, 4 significant findings detected.

Clinical Features | Statistical Tests | METHLYATION CNMF | RNAseq CNMF subtypes | RNAseq cHierClus subtypes | MIRseq CNMF subtypes | MIRseq cHierClus subtypes
Time to Death | logrank test | 0.523 | 0.56 | 0.676 | 0.116 | 0.26
AGE | ANOVA | 0.123 | 0.358 | 0.591 | 0.961 | 0.923
GENDER | Fisher's exact test | 0.626 | 0.59 | 0.362 | 0.0239 | 0.372
HISTOLOGICAL TYPE | Chi-square test | 0.00941 | 0.363 | 0.175 | 0.00398 | 0.0101
PATHOLOGY T | Chi-square test | 0.246 | 0.304 | 0.578 | 0.969 | 0.337
PATHOLOGY N | Chi-square test | 0.418 | 0.509 | 0.148 | 0.561 | 0.781
PATHOLOGICSPREAD(M) | Chi-square test | 0.531 | 0.725 | 0.496 | 0.698 | 0.557
RADIATIONS RADIATION REGIMENINDICATION | Fisher's exact test | 1 |  |  | 0.16 | 0.184
NEOADJUVANT THERAPY | Fisher's exact test | 0.781 |  |  | 0.0861 | 0.517

Clustering Approach #1: 'METHLYATION CNMF'

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

Cluster Labels | 1 | 2 | 3
--- | --- | --- | ---
Number of samples | 19 | 24 | 25

'METHLYATION CNMF' versus 'Time to Death'

P value = 0.523 (logrank test)

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

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 65 | 9 | 0.1 - 70.1 (2.2)
subtype1 | 19 | 4 | 0.1 - 65.1 (4.3)
subtype2 | 23 | 3 | 0.4 - 55.0 (3.6)
subtype3 | 23 | 2 | 0.1 - 70.1 (1.2)

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

'METHLYATION CNMF' versus 'AGE'

P value = 0.123 (ANOVA)

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 66 | 66.8 (11.3)
subtype1 | 19 | 70.0 (11.5)
subtype2 | 22 | 68.0 (10.3)
subtype3 | 25 | 63.3 (11.6)

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

'METHLYATION CNMF' versus 'GENDER'

P value = 0.626 (Fisher's exact test)

Table S4. Clustering Approach #1: 'METHLYATION CNMF' versus Clinical Feature #3: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 24 | 44
subtype1 | 8 | 11
subtype2 | 9 | 15
subtype3 | 7 | 18

Figure S3. Get High-res Image Clustering Approach #1: 'METHLYATION CNMF' versus Clinical Feature #3: 'GENDER'

'METHLYATION CNMF' versus 'HISTOLOGICAL.TYPE'

P value = 0.00941 (Chi-square test)

Table S5. Clustering Approach #1: 'METHLYATION CNMF' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients | STOMACH ADENOCARCINOMA - DIFFUSE TYPE | STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS) | STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE | STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
--- | --- | --- | --- | --- | --- | ---
ALL | 11 | 28 | 3 | 2 | 9 | 15
subtype1 | 4 | 7 | 0 | 0 | 2 | 6
subtype2 | 1 | 8 | 0 | 2 | 7 | 6
subtype3 | 6 | 13 | 3 | 0 | 0 | 3

Figure S4. Get High-res Image Clustering Approach #1: 'METHLYATION CNMF' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'METHLYATION CNMF' versus 'PATHOLOGY.T'

P value = 0.246 (Chi-square test)

Table S6. Clustering Approach #1: 'METHLYATION CNMF' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients | T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 2 | 31 | 29 | 6
subtype1 | 2 | 9 | 6 | 2
subtype2 | 0 | 13 | 9 | 2
subtype3 | 0 | 9 | 14 | 2

Figure S5. Get High-res Image Clustering Approach #1: 'METHLYATION CNMF' versus Clinical Feature #5: 'PATHOLOGY.T'

'METHLYATION CNMF' versus 'PATHOLOGY.N'

P value = 0.418 (Chi-square test)

Table S7. Clustering Approach #1: 'METHLYATION CNMF' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 27 | 21 | 13 | 7
subtype1 | 11 | 5 | 2 | 1
subtype2 | 6 | 9 | 5 | 4
subtype3 | 10 | 7 | 6 | 2

Figure S6. Get High-res Image Clustering Approach #1: 'METHLYATION CNMF' versus Clinical Feature #6: 'PATHOLOGY.N'

'METHLYATION CNMF' versus 'PATHOLOGICSPREAD(M)'

P value = 0.531 (Chi-square test)

Table S8. Clustering Approach #1: 'METHLYATION CNMF' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | MX
--- | --- | --- | ---
ALL | 61 | 6 | 1
subtype1 | 17 | 1 | 1
subtype2 | 22 | 2 | 0
subtype3 | 22 | 3 | 0

Figure S7. Get High-res Image Clustering Approach #1: 'METHLYATION CNMF' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

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

P value = 1 (Fisher's exact test)

Table S9. Clustering Approach #1: 'METHLYATION CNMF' versus Clinical Feature #8: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 66 | 2
subtype1 | 19 | 0
subtype2 | 23 | 1
subtype3 | 24 | 1

Figure S8. Get High-res Image Clustering Approach #1: 'METHLYATION CNMF' versus Clinical Feature #8: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'METHLYATION CNMF' versus 'NEOADJUVANT.THERAPY'

P value = 0.781 (Fisher's exact test)

Table S10. Clustering Approach #1: 'METHLYATION CNMF' versus Clinical Feature #9: 'NEOADJUVANT.THERAPY'

nPatients | NO | YES
--- | --- | ---
ALL | 61 | 7
subtype1 | 18 | 1
subtype2 | 21 | 3
subtype3 | 22 | 3

Figure S9. Get High-res Image Clustering Approach #1: 'METHLYATION CNMF' versus Clinical Feature #9: 'NEOADJUVANT.THERAPY'

Clustering Approach #2: 'RNAseq CNMF subtypes'

Table S11. Get Full Table Description of clustering approach #2: 'RNAseq CNMF subtypes'

Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6
--- | --- | --- | --- | --- | --- | ---
Number of samples | 11 | 6 | 7 | 11 | 12 | 10

'RNAseq CNMF subtypes' versus 'Time to Death'

P value = 0.56 (logrank test)

Table S12. Clustering Approach #2: 'RNAseq CNMF subtypes' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 18 | 5 | 1.0 - 54.0 (14.0)
subtype1 | 2 | 0 | 1.0 - 12.0 (6.5)
subtype2 | 2 | 0 | 1.0 - 18.9 (10.0)
subtype3 | 1 | 0 | 3.0 - 3.0 (3.0)
subtype4 | 2 | 1 | 1.0 - 15.9 (8.5)
subtype5 | 4 | 2 | 4.0 - 30.0 (20.5)
subtype6 | 7 | 2 | 1.0 - 54.0 (27.0)

Figure S10. Get High-res Image Clustering Approach #2: 'RNAseq CNMF subtypes' versus Clinical Feature #1: 'Time to Death'

'RNAseq CNMF subtypes' versus 'AGE'

P value = 0.358 (ANOVA)

Table S13. Clustering Approach #2: 'RNAseq CNMF subtypes' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 57 | 69.5 (10.1)
subtype1 | 11 | 67.0 (12.3)
subtype2 | 6 | 67.3 (12.0)
subtype3 | 7 | 66.7 (8.1)
subtype4 | 11 | 75.6 (9.5)
subtype5 | 12 | 69.2 (9.0)
subtype6 | 10 | 68.9 (9.1)

Figure S11. Get High-res Image Clustering Approach #2: 'RNAseq CNMF subtypes' versus Clinical Feature #2: 'AGE'

'RNAseq CNMF subtypes' versus 'GENDER'

P value = 0.59 (Chi-square test)

Table S14. Clustering Approach #2: 'RNAseq CNMF subtypes' versus Clinical Feature #3: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 30 | 27
subtype1 | 6 | 5
subtype2 | 2 | 4
subtype3 | 2 | 5
subtype4 | 6 | 5
subtype5 | 8 | 4
subtype6 | 6 | 4

Figure S12. Get High-res Image Clustering Approach #2: 'RNAseq CNMF subtypes' versus Clinical Feature #3: 'GENDER'

'RNAseq CNMF subtypes' versus 'HISTOLOGICAL.TYPE'

P value = 0.363 (Chi-square test)

Table S15. Clustering Approach #2: 'RNAseq CNMF subtypes' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients | STOMACH ADENOCARCINOMA - DIFFUSE TYPE | STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS) | STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
--- | --- | --- | --- | --- | ---
ALL | 2 | 39 | 1 | 1 | 9
subtype1 | 0 | 9 | 0 | 0 | 0
subtype2 | 0 | 4 | 0 | 0 | 2
subtype3 | 1 | 6 | 0 | 0 | 0
subtype4 | 0 | 10 | 0 | 0 | 1
subtype5 | 0 | 6 | 1 | 1 | 3
subtype6 | 1 | 4 | 0 | 0 | 3

Figure S13. Get High-res Image Clustering Approach #2: 'RNAseq CNMF subtypes' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'RNAseq CNMF subtypes' versus 'PATHOLOGY.T'

P value = 0.304 (Chi-square test)

Table S16. Clustering Approach #2: 'RNAseq CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients | T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 2 | 14 | 14 | 9
subtype1 | 0 | 1 | 2 | 3
subtype2 | 0 | 2 | 3 | 0
subtype3 | 1 | 1 | 0 | 2
subtype4 | 0 | 3 | 3 | 0
subtype5 | 1 | 2 | 4 | 1
subtype6 | 0 | 5 | 2 | 3

Figure S14. Get High-res Image Clustering Approach #2: 'RNAseq CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY.T'

'RNAseq CNMF subtypes' versus 'PATHOLOGY.N'

P value = 0.509 (Chi-square test)

Table S17. Clustering Approach #2: 'RNAseq CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 8 | 20 | 6 | 5
subtype1 | 1 | 5 | 1 | 1
subtype2 | 2 | 2 | 1 | 0
subtype3 | 1 | 1 | 0 | 1
subtype4 | 1 | 7 | 1 | 0
subtype5 | 1 | 4 | 0 | 1
subtype6 | 2 | 1 | 3 | 2

Figure S15. Get High-res Image Clustering Approach #2: 'RNAseq CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY.N'

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

P value = 0.725 (Chi-square test)

Table S18. Clustering Approach #2: 'RNAseq CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | MX
--- | --- | --- | ---
ALL | 48 | 7 | 2
subtype1 | 10 | 1 | 0
subtype2 | 5 | 0 | 1
subtype3 | 6 | 1 | 0
subtype4 | 10 | 1 | 0
subtype5 | 9 | 2 | 1
subtype6 | 8 | 2 | 0

Figure S16. Get High-res Image Clustering Approach #2: 'RNAseq CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

Clustering Approach #3: 'RNAseq cHierClus subtypes'

Table S19. Get Full Table Description of clustering approach #3: 'RNAseq cHierClus subtypes'

Cluster Labels | 1 | 2 | 3 | 4
--- | --- | --- | --- | ---
Number of samples | 11 | 18 | 17 | 11

'RNAseq cHierClus subtypes' versus 'Time to Death'

P value = 0.676 (logrank test)

Table S20. Clustering Approach #3: 'RNAseq cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 18 | 5 | 1.0 - 54.0 (14.0)
subtype1 | 2 | 0 | 1.0 - 27.0 (14.0)
subtype2 | 5 | 1 | 1.0 - 15.9 (3.0)
subtype3 | 8 | 3 | 1.0 - 54.0 (14.0)
subtype4 | 3 | 1 | 19.1 - 30.0 (22.0)

Figure S17. Get High-res Image Clustering Approach #3: 'RNAseq cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'

'RNAseq cHierClus subtypes' versus 'AGE'

P value = 0.591 (ANOVA)

Table S21. Clustering Approach #3: 'RNAseq cHierClus subtypes' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 57 | 69.5 (10.1)
subtype1 | 11 | 72.1 (10.9)
subtype2 | 18 | 70.1 (11.5)
subtype3 | 17 | 69.3 (8.7)
subtype4 | 11 | 66.2 (9.4)

Figure S18. Get High-res Image Clustering Approach #3: 'RNAseq cHierClus subtypes' versus Clinical Feature #2: 'AGE'

'RNAseq cHierClus subtypes' versus 'GENDER'

P value = 0.362 (Fisher's exact test)

Table S22. Clustering Approach #3: 'RNAseq cHierClus subtypes' versus Clinical Feature #3: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 30 | 27
subtype1 | 4 | 7
subtype2 | 10 | 8
subtype3 | 8 | 9
subtype4 | 8 | 3

Figure S19. Get High-res Image Clustering Approach #3: 'RNAseq cHierClus subtypes' versus Clinical Feature #3: 'GENDER'

'RNAseq cHierClus subtypes' versus 'HISTOLOGICAL.TYPE'

P value = 0.175 (Chi-square test)

Table S23. Clustering Approach #3: 'RNAseq cHierClus subtypes' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients | STOMACH ADENOCARCINOMA - DIFFUSE TYPE | STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS) | STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
--- | --- | --- | --- | --- | ---
ALL | 2 | 39 | 1 | 1 | 9
subtype1 | 0 | 9 | 0 | 0 | 2
subtype2 | 1 | 15 | 0 | 0 | 0
subtype3 | 1 | 9 | 0 | 0 | 5
subtype4 | 0 | 6 | 1 | 1 | 2

Figure S20. Get High-res Image Clustering Approach #3: 'RNAseq cHierClus subtypes' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'RNAseq cHierClus subtypes' versus 'PATHOLOGY.T'

P value = 0.578 (Chi-square test)

Table S24. Clustering Approach #3: 'RNAseq cHierClus subtypes' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients | T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 2 | 14 | 14 | 9
subtype1 | 0 | 3 | 4 | 0
subtype2 | 0 | 2 | 3 | 4
subtype3 | 1 | 5 | 4 | 4
subtype4 | 1 | 4 | 3 | 1

Figure S21. Get High-res Image Clustering Approach #3: 'RNAseq cHierClus subtypes' versus Clinical Feature #5: 'PATHOLOGY.T'

'RNAseq cHierClus subtypes' versus 'PATHOLOGY.N'

P value = 0.148 (Chi-square test)

Table S25. Clustering Approach #3: 'RNAseq cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 8 | 20 | 6 | 5
subtype1 | 3 | 5 | 1 | 0
subtype2 | 0 | 8 | 2 | 2
subtype3 | 3 | 2 | 3 | 3
subtype4 | 2 | 5 | 0 | 0

Figure S22. Get High-res Image Clustering Approach #3: 'RNAseq cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY.N'

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

P value = 0.496 (Chi-square test)

Table S26. Clustering Approach #3: 'RNAseq cHierClus subtypes' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | MX
--- | --- | --- | ---
ALL | 48 | 7 | 2
subtype1 | 10 | 0 | 1
subtype2 | 15 | 3 | 0
subtype3 | 14 | 3 | 0
subtype4 | 9 | 1 | 1

Figure S23. Get High-res Image Clustering Approach #3: 'RNAseq cHierClus subtypes' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

Clustering Approach #4: 'MIRseq CNMF subtypes'

Table S27. Get Full Table Description of clustering approach #4: 'MIRseq CNMF subtypes'

Cluster Labels | 1 | 2 | 3 | 4
--- | --- | --- | --- | ---
Number of samples | 30 | 29 | 30 | 38

'MIRseq CNMF subtypes' versus 'Time to Death'

P value = 0.116 (logrank test)

Table S28. Clustering Approach #4: 'MIRseq CNMF subtypes' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 78 | 14 | 0.1 - 70.1 (4.2)
subtype1 | 27 | 6 | 0.1 - 70.1 (1.7)
subtype2 | 17 | 2 | 0.1 - 65.1 (4.0)
subtype3 | 22 | 3 | 0.3 - 54.0 (4.2)
subtype4 | 12 | 3 | 1.0 - 53.0 (8.0)

Figure S24. Get High-res Image Clustering Approach #4: 'MIRseq CNMF subtypes' versus Clinical Feature #1: 'Time to Death'

'MIRseq CNMF subtypes' versus 'AGE'

P value = 0.961 (ANOVA)

Table S29. Clustering Approach #4: 'MIRseq CNMF subtypes' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 123 | 67.9 (10.8)
subtype1 | 29 | 67.1 (12.6)
subtype2 | 28 | 67.8 (12.4)
subtype3 | 28 | 68.0 (8.8)
subtype4 | 38 | 68.6 (9.6)

Figure S25. Get High-res Image Clustering Approach #4: 'MIRseq CNMF subtypes' versus Clinical Feature #2: 'AGE'

'MIRseq CNMF subtypes' versus 'GENDER'

P value = 0.0239 (Fisher's exact test)

Table S30. Clustering Approach #4: 'MIRseq CNMF subtypes' versus Clinical Feature #3: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 50 | 77
subtype1 | 8 | 22
subtype2 | 7 | 22
subtype3 | 14 | 16
subtype4 | 21 | 17

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

'MIRseq CNMF subtypes' versus 'HISTOLOGICAL.TYPE'

P value = 0.00398 (Chi-square test)

Table S31. Clustering Approach #4: 'MIRseq CNMF subtypes' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients | STOMACH ADENOCARCINOMA - DIFFUSE TYPE | STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS) | STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE | STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
--- | --- | --- | --- | --- | --- | ---
ALL | 12 | 70 | 6 | 2 | 9 | 23
subtype1 | 5 | 11 | 1 | 0 | 3 | 10
subtype2 | 5 | 16 | 3 | 0 | 1 | 2
subtype3 | 1 | 14 | 1 | 2 | 4 | 8
subtype4 | 1 | 29 | 1 | 0 | 1 | 3

Figure S27. Get High-res Image Clustering Approach #4: 'MIRseq CNMF subtypes' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'MIRseq CNMF subtypes' versus 'PATHOLOGY.T'

P value = 0.969 (Chi-square test)

Table S32. Clustering Approach #4: 'MIRseq CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients | T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 4 | 45 | 40 | 17
subtype1 | 2 | 14 | 10 | 4
subtype2 | 0 | 10 | 8 | 5
subtype3 | 1 | 10 | 10 | 4
subtype4 | 1 | 11 | 12 | 4

Figure S28. Get High-res Image Clustering Approach #4: 'MIRseq CNMF subtypes' versus Clinical Feature #5: 'PATHOLOGY.T'

'MIRseq CNMF subtypes' versus 'PATHOLOGY.N'

P value = 0.561 (Chi-square test)

Table S33. Clustering Approach #4: 'MIRseq CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 32 | 46 | 18 | 13
subtype1 | 12 | 10 | 5 | 3
subtype2 | 7 | 11 | 3 | 5
subtype3 | 8 | 9 | 6 | 2
subtype4 | 5 | 16 | 4 | 3

Figure S29. Get High-res Image Clustering Approach #4: 'MIRseq CNMF subtypes' versus Clinical Feature #6: 'PATHOLOGY.N'

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

P value = 0.698 (Chi-square test)

Table S34. Clustering Approach #4: 'MIRseq CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | MX
--- | --- | --- | ---
ALL | 110 | 13 | 4
subtype1 | 25 | 4 | 1
subtype2 | 28 | 1 | 0
subtype3 | 26 | 3 | 1
subtype4 | 31 | 5 | 2

Figure S30. Get High-res Image Clustering Approach #4: 'MIRseq CNMF subtypes' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

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

P value = 0.16 (Fisher's exact test)

Table S35. Clustering Approach #4: 'MIRseq CNMF subtypes' versus Clinical Feature #8: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 123 | 4
subtype1 | 30 | 0
subtype2 | 27 | 2
subtype3 | 28 | 2
subtype4 | 38 | 0

Figure S31. Get High-res Image Clustering Approach #4: 'MIRseq CNMF subtypes' versus Clinical Feature #8: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'MIRseq CNMF subtypes' versus 'NEOADJUVANT.THERAPY'

P value = 0.0861 (Fisher's exact test)

Table S36. Clustering Approach #4: 'MIRseq CNMF subtypes' versus Clinical Feature #9: 'NEOADJUVANT.THERAPY'

nPatients | NO | YES
--- | --- | ---
ALL | 118 | 9
subtype1 | 28 | 2
subtype2 | 25 | 4
subtype3 | 27 | 3
subtype4 | 38 | 0

Figure S32. Get High-res Image Clustering Approach #4: 'MIRseq CNMF subtypes' versus Clinical Feature #9: 'NEOADJUVANT.THERAPY'

Clustering Approach #5: 'MIRseq cHierClus subtypes'

Table S37. Get Full Table Description of clustering approach #5: 'MIRseq cHierClus subtypes'

Cluster Labels | 1 | 2 | 3
--- | --- | --- | ---
Number of samples | 40 | 36 | 51

'MIRseq cHierClus subtypes' versus 'Time to Death'

P value = 0.26 (logrank test)

Table S38. Clustering Approach #5: 'MIRseq cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 78 | 14 | 0.1 - 70.1 (4.2)
subtype1 | 24 | 5 | 0.1 - 70.1 (1.2)
subtype2 | 26 | 4 | 0.3 - 55.0 (4.2)
subtype3 | 28 | 5 | 0.1 - 47.0 (6.0)

Figure S33. Get High-res Image Clustering Approach #5: 'MIRseq cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'

'MIRseq cHierClus subtypes' versus 'AGE'

P value = 0.923 (ANOVA)

Table S39. Clustering Approach #5: 'MIRseq cHierClus subtypes' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 123 | 67.9 (10.8)
subtype1 | 38 | 67.4 (12.2)
subtype2 | 35 | 68.0 (9.2)
subtype3 | 50 | 68.3 (10.8)

Figure S34. Get High-res Image Clustering Approach #5: 'MIRseq cHierClus subtypes' versus Clinical Feature #2: 'AGE'

'MIRseq cHierClus subtypes' versus 'GENDER'

P value = 0.372 (Fisher's exact test)

Table S40. Clustering Approach #5: 'MIRseq cHierClus subtypes' versus Clinical Feature #3: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 50 | 77
subtype1 | 14 | 26
subtype2 | 12 | 24
subtype3 | 24 | 27

Figure S35. Get High-res Image Clustering Approach #5: 'MIRseq cHierClus subtypes' versus Clinical Feature #3: 'GENDER'

'MIRseq cHierClus subtypes' versus 'HISTOLOGICAL.TYPE'

P value = 0.0101 (Chi-square test)

Table S41. Clustering Approach #5: 'MIRseq cHierClus subtypes' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients | STOMACH ADENOCARCINOMA - DIFFUSE TYPE | STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS) | STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE | STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE | STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
--- | --- | --- | --- | --- | --- | ---
ALL | 12 | 70 | 6 | 2 | 9 | 23
subtype1 | 4 | 24 | 4 | 0 | 0 | 6
subtype2 | 2 | 16 | 0 | 2 | 7 | 9
subtype3 | 6 | 30 | 2 | 0 | 2 | 8

Figure S36. Get High-res Image Clustering Approach #5: 'MIRseq cHierClus subtypes' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'MIRseq cHierClus subtypes' versus 'PATHOLOGY.T'

P value = 0.337 (Chi-square test)

Table S42. Clustering Approach #5: 'MIRseq cHierClus subtypes' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients | T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 4 | 45 | 40 | 17
subtype1 | 1 | 14 | 8 | 8
subtype2 | 0 | 14 | 13 | 4
subtype3 | 3 | 17 | 19 | 5

Figure S37. Get High-res Image Clustering Approach #5: 'MIRseq cHierClus subtypes' versus Clinical Feature #5: 'PATHOLOGY.T'

'MIRseq cHierClus subtypes' versus 'PATHOLOGY.N'

P value = 0.781 (Chi-square test)

Table S43. Clustering Approach #5: 'MIRseq cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 32 | 46 | 18 | 13
subtype1 | 11 | 16 | 5 | 3
subtype2 | 10 | 9 | 6 | 5
subtype3 | 11 | 21 | 7 | 5

Figure S38. Get High-res Image Clustering Approach #5: 'MIRseq cHierClus subtypes' versus Clinical Feature #6: 'PATHOLOGY.N'

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

P value = 0.557 (Chi-square test)

Table S44. Clustering Approach #5: 'MIRseq cHierClus subtypes' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | MX
--- | --- | --- | ---
ALL | 110 | 13 | 4
subtype1 | 35 | 5 | 0
subtype2 | 31 | 4 | 1
subtype3 | 44 | 4 | 3

Figure S39. Get High-res Image Clustering Approach #5: 'MIRseq cHierClus subtypes' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

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

P value = 0.184 (Fisher's exact test)

Table S45. Clustering Approach #5: 'MIRseq cHierClus subtypes' versus Clinical Feature #8: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 123 | 4
subtype1 | 38 | 2
subtype2 | 34 | 2
subtype3 | 51 | 0

Figure S40. Get High-res Image Clustering Approach #5: 'MIRseq cHierClus subtypes' versus Clinical Feature #8: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'MIRseq cHierClus subtypes' versus 'NEOADJUVANT.THERAPY'

P value = 0.517 (Fisher's exact test)

Table S46. Clustering Approach #5: 'MIRseq cHierClus subtypes' versus Clinical Feature #9: 'NEOADJUVANT.THERAPY'

nPatients | NO | YES
--- | --- | ---
ALL | 118 | 9
subtype1 | 36 | 4
subtype2 | 33 | 3
subtype3 | 49 | 2

Figure S41. Get High-res Image Clustering Approach #5: 'MIRseq cHierClus subtypes' versus Clinical Feature #9: 'NEOADJUVANT.THERAPY'

Methods & Data
Input

- Cluster data file = STAD.mergedcluster.txt

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

- Number of patients = 136

- Number of clustering approaches = 5

- Number of selected clinical features = 9

- 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)
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