Correlation between aggregated molecular cancer subtypes and selected clinical features

Testicular Germ Cell Tumors (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between aggregated molecular cancer subtypes and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1319TTF

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 8 different clustering approaches and 5 clinical features across 31 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.

3 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes do not correlate to any clinical features.
3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes do not correlate to any clinical features.
CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that do not correlate to any clinical features.
Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 5 subtypes that do not correlate to any clinical features.
3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes do not correlate to any clinical features.
3 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes do not correlate to any clinical features.
3 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes do not correlate to any clinical features.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between subtypes identified by 8 different clustering approaches and 5 clinical features. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, no significant finding detected.


Clinical Features	AGE	NEOPLASM DISEASESTAGE	PATHOLOGY T STAGE	PATHOLOGY N STAGE	ETHNICITY
Statistical Tests	Wilcoxon-test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Copy Number Ratio CNMF subtypes	0.516 (1.00)	0.255 (1.00)	1 (1.00)	0.574 (1.00)	0.578 (1.00)
METHLYATION CNMF	0.309 (1.00)	0.73 (1.00)	0.0917 (1.00)	0.562 (1.00)	1 (1.00)
RNAseq CNMF subtypes	0.587 (1.00)	0.026 (1.00)	0.243 (1.00)	0.788 (1.00)	1 (1.00)
RNAseq cHierClus subtypes	0.642 (1.00)	0.397 (1.00)	0.289 (1.00)	0.274 (1.00)	0.4 (1.00)
MIRSEQ CNMF	0.349 (1.00)	0.0399 (1.00)	1 (1.00)	0.573 (1.00)	1 (1.00)
MIRSEQ CHIERARCHICAL	0.588 (1.00)	0.128 (1.00)	1 (1.00)	0.569 (1.00)	1 (1.00)
MIRseq Mature CNMF subtypes	0.854 (1.00)	0.543 (1.00)	0.454 (1.00)	0.467 (1.00)	1 (1.00)
MIRseq Mature cHierClus subtypes	0.368 (1.00)	0.141 (1.00)	1 (1.00)	0.1 (1.00)	0.429 (1.00)

Clustering Approach #1: 'Copy Number Ratio CNMF subtypes'

Table S1. Description of clustering approach #1: 'Copy Number Ratio CNMF subtypes'

Cluster Labels	1	2	3
Number of samples	7	7	17

'Copy Number Ratio CNMF subtypes' versus 'AGE'

P value = 0.516 (Kruskal-Wallis (anova)), Q value = 1

Table S2. Clustering Approach #1: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #1: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	31	30.7 (8.4)
subtype1	7	33.0 (5.8)
subtype2	7	29.3 (8.0)
subtype3	17	30.3 (9.7)

Figure S1. Get High-res Image Clustering Approach #1: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #1: 'AGE'

'Copy Number Ratio CNMF subtypes' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.255 (Fisher's exact test), Q value = 1

Table S3. Clustering Approach #1: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #2: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE IA	STAGE IB	STAGE II	STAGE IIA	STAGE IIC	STAGE III	STAGE IIIB	STAGE IIIC	STAGE IS
ALL	5	1	2	3	1	1	2	2	1	13
subtype1	1	1	1	0	1	1	0	0	0	2
subtype2	3	0	0	0	0	0	1	0	0	3
subtype3	1	0	1	3	0	0	1	2	1	8

Figure S2. Get High-res Image Clustering Approach #1: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #2: 'NEOPLASM.DISEASESTAGE'

'Copy Number Ratio CNMF subtypes' versus 'PATHOLOGY.T.STAGE'

P value = 1 (Fisher's exact test), Q value = 1

Table S4. Clustering Approach #1: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2+T3
ALL	15	16
subtype1	3	4
subtype2	4	3
subtype3	8	9

Figure S3. Get High-res Image Clustering Approach #1: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

'Copy Number Ratio CNMF subtypes' versus 'PATHOLOGY.N.STAGE'

P value = 0.574 (Fisher's exact test), Q value = 1

Table S5. Clustering Approach #1: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGY.N.STAGE'

nPatients	0	1
ALL	13	4
subtype1	2	1
subtype2	4	0
subtype3	7	3

Figure S4. Get High-res Image Clustering Approach #1: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGY.N.STAGE'

'Copy Number Ratio CNMF subtypes' versus 'ETHNICITY'

P value = 0.578 (Fisher's exact test), Q value = 1

Table S6. Clustering Approach #1: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #5: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	3	28
subtype1	1	6
subtype2	1	6
subtype3	1	16

Figure S5. Get High-res Image Clustering Approach #1: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #5: 'ETHNICITY'

Clustering Approach #2: 'METHLYATION CNMF'

Table S7. Description of clustering approach #2: 'METHLYATION CNMF'

Cluster Labels	1	2	3
Number of samples	6	14	11

'METHLYATION CNMF' versus 'AGE'

P value = 0.309 (Kruskal-Wallis (anova)), Q value = 1

Table S8. Clustering Approach #2: 'METHLYATION CNMF' versus Clinical Feature #1: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	31	30.7 (8.4)
subtype1	6	34.8 (7.8)
subtype2	14	28.9 (8.5)
subtype3	11	30.6 (8.6)

Figure S6. Get High-res Image Clustering Approach #2: 'METHLYATION CNMF' versus Clinical Feature #1: 'AGE'

'METHLYATION CNMF' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.73 (Fisher's exact test), Q value = 1

Table S9. Clustering Approach #2: 'METHLYATION CNMF' versus Clinical Feature #2: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE IA	STAGE IB	STAGE II	STAGE IIA	STAGE IIC	STAGE III	STAGE IIIB	STAGE IIIC	STAGE IS
ALL	5	1	2	3	1	1	2	2	1	13
subtype1	1	0	1	0	0	1	0	1	0	2
subtype2	1	1	1	1	1	0	1	1	0	7
subtype3	3	0	0	2	0	0	1	0	1	4

Figure S7. Get High-res Image Clustering Approach #2: 'METHLYATION CNMF' versus Clinical Feature #2: 'NEOPLASM.DISEASESTAGE'

'METHLYATION CNMF' versus 'PATHOLOGY.T.STAGE'

P value = 0.0917 (Fisher's exact test), Q value = 1

Table S10. Clustering Approach #2: 'METHLYATION CNMF' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2+T3
ALL	15	16
subtype1	3	3
subtype2	4	10
subtype3	8	3

Figure S8. Get High-res Image Clustering Approach #2: 'METHLYATION CNMF' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

'METHLYATION CNMF' versus 'PATHOLOGY.N.STAGE'

P value = 0.562 (Fisher's exact test), Q value = 1

Table S11. Clustering Approach #2: 'METHLYATION CNMF' versus Clinical Feature #4: 'PATHOLOGY.N.STAGE'

nPatients	0	1
ALL	13	4
subtype1	1	1
subtype2	7	2
subtype3	5	1

Figure S9. Get High-res Image Clustering Approach #2: 'METHLYATION CNMF' versus Clinical Feature #4: 'PATHOLOGY.N.STAGE'

'METHLYATION CNMF' versus 'ETHNICITY'

P value = 1 (Fisher's exact test), Q value = 1

Table S12. Clustering Approach #2: 'METHLYATION CNMF' versus Clinical Feature #5: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	3	28
subtype1	0	6
subtype2	2	12
subtype3	1	10

Figure S10. Get High-res Image Clustering Approach #2: 'METHLYATION CNMF' versus Clinical Feature #5: 'ETHNICITY'

Clustering Approach #3: 'RNAseq CNMF subtypes'

Table S13. Description of clustering approach #3: 'RNAseq CNMF subtypes'

Cluster Labels	1	2	3
Number of samples	10	11	10

'RNAseq CNMF subtypes' versus 'AGE'

P value = 0.587 (Kruskal-Wallis (anova)), Q value = 1

Table S14. Clustering Approach #3: 'RNAseq CNMF subtypes' versus Clinical Feature #1: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	31	30.7 (8.4)
subtype1	10	32.4 (7.6)
subtype2	11	28.7 (9.3)
subtype3	10	31.1 (8.6)

Figure S11. Get High-res Image Clustering Approach #3: 'RNAseq CNMF subtypes' versus Clinical Feature #1: 'AGE'

'RNAseq CNMF subtypes' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.026 (Fisher's exact test), Q value = 1

Table S15. Clustering Approach #3: 'RNAseq CNMF subtypes' versus Clinical Feature #2: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE IA	STAGE IB	STAGE II	STAGE IIA	STAGE IIC	STAGE III	STAGE IIIB	STAGE IIIC	STAGE IS
ALL	5	1	2	3	1	1	2	2	1	13
subtype1	5	0	1	0	0	1	0	1	0	2
subtype2	0	1	1	1	0	0	1	1	0	6
subtype3	0	0	0	2	1	0	1	0	1	5

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

'RNAseq CNMF subtypes' versus 'PATHOLOGY.T.STAGE'

P value = 0.243 (Fisher's exact test), Q value = 1

Table S16. Clustering Approach #3: 'RNAseq CNMF subtypes' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2+T3
ALL	15	16
subtype1	6	4
subtype2	3	8
subtype3	6	4

Figure S13. Get High-res Image Clustering Approach #3: 'RNAseq CNMF subtypes' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

'RNAseq CNMF subtypes' versus 'PATHOLOGY.N.STAGE'

P value = 0.788 (Fisher's exact test), Q value = 1

Table S17. Clustering Approach #3: 'RNAseq CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGY.N.STAGE'

nPatients	0	1
ALL	13	4
subtype1	3	1
subtype2	6	1
subtype3	4	2

Figure S14. Get High-res Image Clustering Approach #3: 'RNAseq CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGY.N.STAGE'

'RNAseq CNMF subtypes' versus 'ETHNICITY'

P value = 1 (Fisher's exact test), Q value = 1

Table S18. Clustering Approach #3: 'RNAseq CNMF subtypes' versus Clinical Feature #5: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	3	28
subtype1	1	9
subtype2	1	10
subtype3	1	9

Figure S15. Get High-res Image Clustering Approach #3: 'RNAseq CNMF subtypes' versus Clinical Feature #5: 'ETHNICITY'

Clustering Approach #4: 'RNAseq cHierClus subtypes'

Table S19. Description of clustering approach #4: 'RNAseq cHierClus subtypes'

Cluster Labels	1	2	3	4	5	6	7
Number of samples	6	4	2	5	2	8	4

'RNAseq cHierClus subtypes' versus 'AGE'

P value = 0.642 (Kruskal-Wallis (anova)), Q value = 1

Table S20. Clustering Approach #4: 'RNAseq cHierClus subtypes' versus Clinical Feature #1: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	27	30.9 (8.8)
subtype1	6	34.0 (8.9)
subtype2	4	30.0 (5.6)
subtype4	5	27.4 (5.9)
subtype6	8	29.1 (10.6)
subtype7	4	35.2 (11.4)

Figure S16. Get High-res Image Clustering Approach #4: 'RNAseq cHierClus subtypes' versus Clinical Feature #1: 'AGE'

'RNAseq cHierClus subtypes' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.397 (Fisher's exact test), Q value = 1

Table S21. Clustering Approach #4: 'RNAseq cHierClus subtypes' versus Clinical Feature #2: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE IA	STAGE IB	STAGE II	STAGE IIA	STAGE IIC	STAGE III	STAGE IIIB	STAGE IIIC	STAGE IS
ALL	5	1	1	3	1	1	2	2	1	10
subtype1	2	0	1	0	0	1	0	1	0	1
subtype2	3	0	0	0	0	0	0	0	0	1
subtype4	0	0	0	1	1	0	0	0	1	2
subtype6	0	1	0	1	0	0	1	1	0	4
subtype7	0	0	0	1	0	0	1	0	0	2

Figure S17. Get High-res Image Clustering Approach #4: 'RNAseq cHierClus subtypes' versus Clinical Feature #2: 'NEOPLASM.DISEASESTAGE'

'RNAseq cHierClus subtypes' versus 'PATHOLOGY.T.STAGE'

P value = 0.289 (Fisher's exact test), Q value = 1

Table S22. Clustering Approach #4: 'RNAseq cHierClus subtypes' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2+T3
ALL	14	13
subtype1	2	4
subtype2	4	0
subtype4	3	2
subtype6	3	5
subtype7	2	2

Figure S18. Get High-res Image Clustering Approach #4: 'RNAseq cHierClus subtypes' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

'RNAseq cHierClus subtypes' versus 'PATHOLOGY.N.STAGE'

P value = 0.274 (Fisher's exact test), Q value = 1

Table S23. Clustering Approach #4: 'RNAseq cHierClus subtypes' versus Clinical Feature #4: 'PATHOLOGY.N.STAGE'

nPatients	0	1
ALL	11	4
subtype1	0	1
subtype2	3	0
subtype4	2	2
subtype6	5	1
subtype7	1	0

Figure S19. Get High-res Image Clustering Approach #4: 'RNAseq cHierClus subtypes' versus Clinical Feature #4: 'PATHOLOGY.N.STAGE'

'RNAseq cHierClus subtypes' versus 'ETHNICITY'

P value = 0.4 (Fisher's exact test), Q value = 1

Table S24. Clustering Approach #4: 'RNAseq cHierClus subtypes' versus Clinical Feature #5: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	2	25
subtype1	1	5
subtype2	0	4
subtype4	0	5
subtype6	0	8
subtype7	1	3

Figure S20. Get High-res Image Clustering Approach #4: 'RNAseq cHierClus subtypes' versus Clinical Feature #5: 'ETHNICITY'

Clustering Approach #5: 'MIRSEQ CNMF'

Table S25. Description of clustering approach #5: 'MIRSEQ CNMF'

Cluster Labels	1	2	3	4
Number of samples	2	4	4	3

'MIRSEQ CNMF' versus 'AGE'

P value = 0.349 (Kruskal-Wallis (anova)), Q value = 1

Table S26. Clustering Approach #5: 'MIRSEQ CNMF' versus Clinical Feature #1: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	11	31.5 (7.7)
subtype2	4	32.5 (7.0)
subtype3	4	27.5 (6.6)
subtype4	3	35.3 (10.0)

Figure S21. Get High-res Image Clustering Approach #5: 'MIRSEQ CNMF' versus Clinical Feature #1: 'AGE'

'MIRSEQ CNMF' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.0399 (Fisher's exact test), Q value = 1

Table S27. Clustering Approach #5: 'MIRSEQ CNMF' versus Clinical Feature #2: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE IB	STAGE IIA	STAGE IIC	STAGE IIIC	STAGE IS
ALL	1	1	1	1	1	6
subtype2	0	0	0	0	0	4
subtype3	0	0	1	0	1	2
subtype4	1	1	0	1	0	0

Figure S22. Get High-res Image Clustering Approach #5: 'MIRSEQ CNMF' versus Clinical Feature #2: 'NEOPLASM.DISEASESTAGE'

'MIRSEQ CNMF' versus 'PATHOLOGY.T.STAGE'

P value = 1 (Fisher's exact test), Q value = 1

Table S28. Clustering Approach #5: 'MIRSEQ CNMF' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2+T3
ALL	4	7
subtype2	1	3
subtype3	2	2
subtype4	1	2

Figure S23. Get High-res Image Clustering Approach #5: 'MIRSEQ CNMF' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

'MIRSEQ CNMF' versus 'PATHOLOGY.N.STAGE'

P value = 0.573 (Fisher's exact test), Q value = 1

Table S29. Clustering Approach #5: 'MIRSEQ CNMF' versus Clinical Feature #4: 'PATHOLOGY.N.STAGE'

nPatients	0	1
ALL	5	2
subtype2	3	0
subtype3	1	2
subtype4	1	0

Figure S24. Get High-res Image Clustering Approach #5: 'MIRSEQ CNMF' versus Clinical Feature #4: 'PATHOLOGY.N.STAGE'

'MIRSEQ CNMF' versus 'ETHNICITY'

P value = 1 (Fisher's exact test), Q value = 1

Table S30. Clustering Approach #5: 'MIRSEQ CNMF' versus Clinical Feature #5: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	1	10
subtype2	0	4
subtype3	1	3
subtype4	0	3

Figure S25. Get High-res Image Clustering Approach #5: 'MIRSEQ CNMF' versus Clinical Feature #5: 'ETHNICITY'

Clustering Approach #6: 'MIRSEQ CHIERARCHICAL'

Table S31. Description of clustering approach #6: 'MIRSEQ CHIERARCHICAL'

Cluster Labels	1	2	3
Number of samples	5	4	4

'MIRSEQ CHIERARCHICAL' versus 'AGE'

P value = 0.588 (Kruskal-Wallis (anova)), Q value = 1

Table S32. Clustering Approach #6: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #1: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	13	30.9 (7.4)
subtype1	5	32.4 (8.9)
subtype2	4	32.5 (7.0)
subtype3	4	27.5 (6.6)

Figure S26. Get High-res Image Clustering Approach #6: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #1: 'AGE'

'MIRSEQ CHIERARCHICAL' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.128 (Fisher's exact test), Q value = 1

Table S33. Clustering Approach #6: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #2: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE IB	STAGE IIA	STAGE IIC	STAGE IIIC	STAGE IS
ALL	2	1	1	1	1	7
subtype1	2	1	0	1	0	1
subtype2	0	0	0	0	0	4
subtype3	0	0	1	0	1	2

Figure S27. Get High-res Image Clustering Approach #6: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #2: 'NEOPLASM.DISEASESTAGE'

'MIRSEQ CHIERARCHICAL' versus 'PATHOLOGY.T.STAGE'

P value = 1 (Fisher's exact test), Q value = 1

Table S34. Clustering Approach #6: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2+T3
ALL	5	8
subtype1	2	3
subtype2	1	3
subtype3	2	2

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

'MIRSEQ CHIERARCHICAL' versus 'PATHOLOGY.N.STAGE'

P value = 0.569 (Fisher's exact test), Q value = 1

Table S35. Clustering Approach #6: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #4: 'PATHOLOGY.N.STAGE'

nPatients	0	1
ALL	5	2
subtype1	1	0
subtype2	3	0
subtype3	1	2

Figure S29. Get High-res Image Clustering Approach #6: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #4: 'PATHOLOGY.N.STAGE'

'MIRSEQ CHIERARCHICAL' versus 'ETHNICITY'

P value = 1 (Fisher's exact test), Q value = 1

Table S36. Clustering Approach #6: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #5: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	2	11
subtype1	1	4
subtype2	0	4
subtype3	1	3

Figure S30. Get High-res Image Clustering Approach #6: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #5: 'ETHNICITY'

Clustering Approach #7: 'MIRseq Mature CNMF subtypes'

Table S37. Description of clustering approach #7: 'MIRseq Mature CNMF subtypes'

Cluster Labels	1	2	3	4
Number of samples	2	3	3	5

'MIRseq Mature CNMF subtypes' versus 'AGE'

P value = 0.854 (Kruskal-Wallis (anova)), Q value = 1

Table S38. Clustering Approach #7: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #1: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	11	30.2 (6.5)
subtype2	3	32.3 (8.5)
subtype3	3	30.7 (6.8)
subtype4	5	28.6 (6.2)

Figure S31. Get High-res Image Clustering Approach #7: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #1: 'AGE'

'MIRseq Mature CNMF subtypes' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.543 (Fisher's exact test), Q value = 1

Table S39. Clustering Approach #7: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #2: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE IIA	STAGE IIC	STAGE IIIC	STAGE IS
ALL	1	1	1	1	7
subtype2	0	0	0	0	3
subtype3	1	0	1	0	1
subtype4	0	1	0	1	3

Figure S32. Get High-res Image Clustering Approach #7: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #2: 'NEOPLASM.DISEASESTAGE'

'MIRseq Mature CNMF subtypes' versus 'PATHOLOGY.T.STAGE'

P value = 0.454 (Fisher's exact test), Q value = 1

Table S40. Clustering Approach #7: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2+T3
ALL	4	7
subtype2	0	3
subtype3	1	2
subtype4	3	2

Figure S33. Get High-res Image Clustering Approach #7: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

'MIRseq Mature CNMF subtypes' versus 'PATHOLOGY.N.STAGE'

P value = 0.467 (Fisher's exact test), Q value = 1

Table S41. Clustering Approach #7: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGY.N.STAGE'

nPatients	0	1
ALL	4	2
subtype2	2	0
subtype3	0	0
subtype4	2	2

Figure S34. Get High-res Image Clustering Approach #7: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #4: 'PATHOLOGY.N.STAGE'

'MIRseq Mature CNMF subtypes' versus 'ETHNICITY'

P value = 1 (Fisher's exact test), Q value = 1

Table S42. Clustering Approach #7: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #5: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	2	9
subtype2	0	3
subtype3	1	2
subtype4	1	4

Figure S35. Get High-res Image Clustering Approach #7: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #5: 'ETHNICITY'

Clustering Approach #8: 'MIRseq Mature cHierClus subtypes'

Table S43. Description of clustering approach #8: 'MIRseq Mature cHierClus subtypes'

Cluster Labels	1	2	3	4	5	6	7
Number of samples	1	1	4	3	1	1	2

'MIRseq Mature cHierClus subtypes' versus 'AGE'

P value = 0.368 (Wilcoxon-test), Q value = 1

Table S44. Clustering Approach #8: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #1: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	7	29.6 (7.2)
subtype3	4	32.5 (7.0)
subtype4	3	25.7 (6.7)

Figure S36. Get High-res Image Clustering Approach #8: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #1: 'AGE'

'MIRseq Mature cHierClus subtypes' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.141 (Fisher's exact test), Q value = 1

Table S45. Clustering Approach #8: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #2: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE IIA	STAGE IIIC	STAGE IS
ALL	1	1	5
subtype3	0	0	4
subtype4	1	1	1

Figure S37. Get High-res Image Clustering Approach #8: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #2: 'NEOPLASM.DISEASESTAGE'

'MIRseq Mature cHierClus subtypes' versus 'PATHOLOGY.T.STAGE'

P value = 1 (Fisher's exact test), Q value = 1

Table S46. Clustering Approach #8: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2+T3
ALL	2	5
subtype3	1	3
subtype4	1	2

Figure S38. Get High-res Image Clustering Approach #8: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

'MIRseq Mature cHierClus subtypes' versus 'PATHOLOGY.N.STAGE'

P value = 0.1 (Fisher's exact test), Q value = 1

Table S47. Clustering Approach #8: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #4: 'PATHOLOGY.N.STAGE'

nPatients	0	1
ALL	3	2
subtype3	3	0
subtype4	0	2

Figure S39. Get High-res Image Clustering Approach #8: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #4: 'PATHOLOGY.N.STAGE'

'MIRseq Mature cHierClus subtypes' versus 'ETHNICITY'

P value = 0.429 (Fisher's exact test), Q value = 1

Table S48. Clustering Approach #8: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #5: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	1	6
subtype3	0	4
subtype4	1	2

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

Methods & Data

Input

Cluster data file = TGCT-TP.mergedcluster.txt
Clinical data file = TGCT-TP.merged_data.txt
Number of patients = 31
Number of clustering approaches = 8
Number of selected clinical features = 5
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)

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

Q value calculation

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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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] 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)

[4] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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