Correlation between aggregated molecular cancer subtypes and selected clinical features
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (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/C19G5KN4
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 4 clinical features across 35 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.

  • 2 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes do not correlate to any clinical features.

  • 2 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 2 subtypes that do not correlate to any clinical features.

  • Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that do not correlate to any clinical features.

  • 4 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes do not correlate to any clinical features.

  • 5 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes do not correlate to any clinical features.

  • 7 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 4 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
Time
to
Death
AGE GENDER RACE
Statistical Tests logrank test Kruskal-Wallis (anova) Fisher's exact test Fisher's exact test
Copy Number Ratio CNMF subtypes 0.171
(1.00)
0.84
(1.00)
0.305
(1.00)
0.48
(1.00)
METHLYATION CNMF 0.188
(1.00)
0.552
(1.00)
0.74
(1.00)
0.124
(1.00)
RNAseq CNMF subtypes 0.0717
(1.00)
0.181
(1.00)
0.128
(1.00)
0.169
(1.00)
RNAseq cHierClus subtypes 0.0591
(1.00)
0.456
(1.00)
0.386
(1.00)
0.622
(1.00)
MIRSEQ CNMF 0.129
(1.00)
0.79
(1.00)
0.181
(1.00)
0.133
(1.00)
MIRSEQ CHIERARCHICAL 0.34
(1.00)
0.435
(1.00)
0.154
(1.00)
0.881
(1.00)
MIRseq Mature CNMF subtypes 0.0702
(1.00)
0.904
(1.00)
0.149
(1.00)
0.151
(1.00)
MIRseq Mature cHierClus subtypes 0.4
(1.00)
0.829
(1.00)
0.211
(1.00)
0.2
(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
Number of samples 21 14
'Copy Number Ratio CNMF subtypes' versus 'Time to Death'

P value = 0.171 (logrank test), Q value = 1

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

nPatients nDeath Duration Range (Median), Month
ALL 34 5 0.2 - 211.2 (26.0)
subtype1 20 5 0.2 - 211.2 (26.0)
subtype2 14 0 0.2 - 196.6 (26.0)

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

'Copy Number Ratio CNMF subtypes' versus 'AGE'

P value = 0.84 (Wilcoxon-test), Q value = 1

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

nPatients Mean (Std.Dev)
ALL 35 57.1 (11.9)
subtype1 21 57.6 (12.1)
subtype2 14 56.5 (12.1)

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

'Copy Number Ratio CNMF subtypes' versus 'GENDER'

P value = 0.305 (Fisher's exact test), Q value = 1

Table S4.  Clustering Approach #1: 'Copy Number Ratio CNMF subtypes' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 18 17
subtype1 9 12
subtype2 9 5

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

'Copy Number Ratio CNMF subtypes' versus 'RACE'

P value = 0.48 (Fisher's exact test), Q value = 1

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

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 18 1 16
subtype1 9 1 11
subtype2 9 0 5

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

Clustering Approach #2: 'METHLYATION CNMF'

Table S6.  Description of clustering approach #2: 'METHLYATION CNMF'

Cluster Labels 1 2
Number of samples 17 18
'METHLYATION CNMF' versus 'Time to Death'

P value = 0.188 (logrank test), Q value = 1

Table S7.  Clustering Approach #2: 'METHLYATION CNMF' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 34 5 0.2 - 211.2 (26.0)
subtype1 16 1 0.2 - 196.6 (38.6)
subtype2 18 4 0.7 - 211.2 (17.3)

Figure S5.  Get High-res Image Clustering Approach #2: 'METHLYATION CNMF' versus Clinical Feature #1: 'Time to Death'

'METHLYATION CNMF' versus 'AGE'

P value = 0.552 (Wilcoxon-test), Q value = 1

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

nPatients Mean (Std.Dev)
ALL 35 57.1 (11.9)
subtype1 17 58.8 (11.1)
subtype2 18 55.6 (12.8)

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

'METHLYATION CNMF' versus 'GENDER'

P value = 0.74 (Fisher's exact test), Q value = 1

Table S9.  Clustering Approach #2: 'METHLYATION CNMF' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 18 17
subtype1 8 9
subtype2 10 8

Figure S7.  Get High-res Image Clustering Approach #2: 'METHLYATION CNMF' versus Clinical Feature #3: 'GENDER'

'METHLYATION CNMF' versus 'RACE'

P value = 0.124 (Fisher's exact test), Q value = 1

Table S10.  Clustering Approach #2: 'METHLYATION CNMF' versus Clinical Feature #4: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 18 1 16
subtype1 6 1 10
subtype2 12 0 6

Figure S8.  Get High-res Image Clustering Approach #2: 'METHLYATION CNMF' versus Clinical Feature #4: 'RACE'

Clustering Approach #3: 'RNAseq CNMF subtypes'

Table S11.  Description of clustering approach #3: 'RNAseq CNMF subtypes'

Cluster Labels 1 2
Number of samples 14 13
'RNAseq CNMF subtypes' versus 'Time to Death'

P value = 0.0717 (logrank test), Q value = 1

Table S12.  Clustering Approach #3: 'RNAseq CNMF subtypes' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 27 4 0.2 - 211.2 (31.7)
subtype1 14 2 4.3 - 211.2 (41.8)
subtype2 13 2 0.2 - 98.1 (22.3)

Figure S9.  Get High-res Image Clustering Approach #3: 'RNAseq CNMF subtypes' versus Clinical Feature #1: 'Time to Death'

'RNAseq CNMF subtypes' versus 'AGE'

P value = 0.181 (Wilcoxon-test), Q value = 1

Table S13.  Clustering Approach #3: 'RNAseq CNMF subtypes' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 27 56.3 (12.4)
subtype1 14 59.9 (10.3)
subtype2 13 52.4 (13.7)

Figure S10.  Get High-res Image Clustering Approach #3: 'RNAseq CNMF subtypes' versus Clinical Feature #2: 'AGE'

'RNAseq CNMF subtypes' versus 'GENDER'

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

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

nPatients FEMALE MALE
ALL 14 13
subtype1 5 9
subtype2 9 4

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

'RNAseq CNMF subtypes' versus 'RACE'

P value = 0.169 (Fisher's exact test), Q value = 1

Table S15.  Clustering Approach #3: 'RNAseq CNMF subtypes' versus Clinical Feature #4: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 11 1 15
subtype1 4 0 10
subtype2 7 1 5

Figure S12.  Get High-res Image Clustering Approach #3: 'RNAseq CNMF subtypes' versus Clinical Feature #4: 'RACE'

Clustering Approach #4: 'RNAseq cHierClus subtypes'

Table S16.  Description of clustering approach #4: 'RNAseq cHierClus subtypes'

Cluster Labels 1 2 3
Number of samples 13 10 4
'RNAseq cHierClus subtypes' versus 'Time to Death'

P value = 0.0591 (logrank test), Q value = 1

Table S17.  Clustering Approach #4: 'RNAseq cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 27 4 0.2 - 211.2 (31.7)
subtype1 13 2 4.3 - 211.2 (35.5)
subtype2 10 2 0.2 - 98.1 (12.1)
subtype3 4 0 15.0 - 57.2 (39.4)

Figure S13.  Get High-res Image Clustering Approach #4: 'RNAseq cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'

'RNAseq cHierClus subtypes' versus 'AGE'

P value = 0.456 (Kruskal-Wallis (anova)), Q value = 1

Table S18.  Clustering Approach #4: 'RNAseq cHierClus subtypes' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 27 56.3 (12.4)
subtype1 13 58.8 (12.7)
subtype2 10 54.7 (13.0)
subtype3 4 52.2 (11.6)

Figure S14.  Get High-res Image Clustering Approach #4: 'RNAseq cHierClus subtypes' versus Clinical Feature #2: 'AGE'

'RNAseq cHierClus subtypes' versus 'GENDER'

P value = 0.386 (Fisher's exact test), Q value = 1

Table S19.  Clustering Approach #4: 'RNAseq cHierClus subtypes' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 14 13
subtype1 5 8
subtype2 6 4
subtype3 3 1

Figure S15.  Get High-res Image Clustering Approach #4: 'RNAseq cHierClus subtypes' versus Clinical Feature #3: 'GENDER'

'RNAseq cHierClus subtypes' versus 'RACE'

P value = 0.622 (Fisher's exact test), Q value = 1

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

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 11 1 15
subtype1 5 0 8
subtype2 5 1 4
subtype3 1 0 3

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

Clustering Approach #5: 'MIRSEQ CNMF'

Table S21.  Description of clustering approach #5: 'MIRSEQ CNMF'

Cluster Labels 1 2 3 4
Number of samples 11 8 5 10
'MIRSEQ CNMF' versus 'Time to Death'

P value = 0.129 (logrank test), Q value = 1

Table S22.  Clustering Approach #5: 'MIRSEQ CNMF' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 33 5 0.2 - 211.2 (25.9)
subtype1 11 1 0.7 - 211.2 (25.9)
subtype2 7 1 0.2 - 43.9 (22.3)
subtype3 5 1 9.8 - 26.0 (12.7)
subtype4 10 2 4.1 - 106.1 (33.6)

Figure S17.  Get High-res Image Clustering Approach #5: 'MIRSEQ CNMF' versus Clinical Feature #1: 'Time to Death'

'MIRSEQ CNMF' versus 'AGE'

P value = 0.79 (Kruskal-Wallis (anova)), Q value = 1

Table S23.  Clustering Approach #5: 'MIRSEQ CNMF' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 34 57.2 (12.1)
subtype1 11 58.0 (9.9)
subtype2 8 58.1 (10.2)
subtype3 5 61.4 (11.9)
subtype4 10 53.4 (16.1)

Figure S18.  Get High-res Image Clustering Approach #5: 'MIRSEQ CNMF' versus Clinical Feature #2: 'AGE'

'MIRSEQ CNMF' versus 'GENDER'

P value = 0.181 (Fisher's exact test), Q value = 1

Table S24.  Clustering Approach #5: 'MIRSEQ CNMF' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 17 17
subtype1 4 7
subtype2 6 2
subtype3 1 4
subtype4 6 4

Figure S19.  Get High-res Image Clustering Approach #5: 'MIRSEQ CNMF' versus Clinical Feature #3: 'GENDER'

'MIRSEQ CNMF' versus 'RACE'

P value = 0.133 (Fisher's exact test), Q value = 1

Table S25.  Clustering Approach #5: 'MIRSEQ CNMF' versus Clinical Feature #4: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 18 1 15
subtype1 5 0 6
subtype2 4 1 3
subtype3 5 0 0
subtype4 4 0 6

Figure S20.  Get High-res Image Clustering Approach #5: 'MIRSEQ CNMF' versus Clinical Feature #4: 'RACE'

Clustering Approach #6: 'MIRSEQ CHIERARCHICAL'

Table S26.  Description of clustering approach #6: 'MIRSEQ CHIERARCHICAL'

Cluster Labels 1 2 3 4 5
Number of samples 9 9 5 5 6
'MIRSEQ CHIERARCHICAL' versus 'Time to Death'

P value = 0.34 (logrank test), Q value = 1

Table S27.  Clustering Approach #6: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 33 5 0.2 - 211.2 (25.9)
subtype1 9 1 4.3 - 211.2 (31.1)
subtype2 8 2 0.2 - 106.1 (31.7)
subtype3 5 0 0.7 - 196.6 (15.0)
subtype4 5 1 9.8 - 57.2 (13.5)
subtype5 6 1 4.1 - 98.1 (25.6)

Figure S21.  Get High-res Image Clustering Approach #6: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #1: 'Time to Death'

'MIRSEQ CHIERARCHICAL' versus 'AGE'

P value = 0.435 (Kruskal-Wallis (anova)), Q value = 1

Table S28.  Clustering Approach #6: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 34 57.2 (12.1)
subtype1 9 56.3 (10.4)
subtype2 9 59.1 (10.0)
subtype3 5 55.8 (11.3)
subtype4 5 65.4 (8.2)
subtype5 6 49.8 (18.3)

Figure S22.  Get High-res Image Clustering Approach #6: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #2: 'AGE'

'MIRSEQ CHIERARCHICAL' versus 'GENDER'

P value = 0.154 (Fisher's exact test), Q value = 1

Table S29.  Clustering Approach #6: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 17 17
subtype1 2 7
subtype2 6 3
subtype3 2 3
subtype4 2 3
subtype5 5 1

Figure S23.  Get High-res Image Clustering Approach #6: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #3: 'GENDER'

'MIRSEQ CHIERARCHICAL' versus 'RACE'

P value = 0.881 (Fisher's exact test), Q value = 1

Table S30.  Clustering Approach #6: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #4: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 18 1 15
subtype1 4 0 5
subtype2 4 1 4
subtype3 3 0 2
subtype4 4 0 1
subtype5 3 0 3

Figure S24.  Get High-res Image Clustering Approach #6: 'MIRSEQ CHIERARCHICAL' versus Clinical Feature #4: 'RACE'

Clustering Approach #7: 'MIRseq Mature CNMF subtypes'

Table S31.  Description of clustering approach #7: 'MIRseq Mature CNMF subtypes'

Cluster Labels 1 2
Number of samples 13 18
'MIRseq Mature CNMF subtypes' versus 'Time to Death'

P value = 0.0702 (logrank test), Q value = 1

Table S32.  Clustering Approach #7: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 30 5 0.2 - 211.2 (26.0)
subtype1 13 1 0.7 - 211.2 (24.7)
subtype2 17 4 0.2 - 106.1 (35.5)

Figure S25.  Get High-res Image Clustering Approach #7: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #1: 'Time to Death'

'MIRseq Mature CNMF subtypes' versus 'AGE'

P value = 0.904 (Wilcoxon-test), Q value = 1

Table S33.  Clustering Approach #7: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 31 56.3 (12.2)
subtype1 13 56.5 (11.0)
subtype2 18 56.2 (13.3)

Figure S26.  Get High-res Image Clustering Approach #7: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #2: 'AGE'

'MIRseq Mature CNMF subtypes' versus 'GENDER'

P value = 0.149 (Fisher's exact test), Q value = 1

Table S34.  Clustering Approach #7: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 15 16
subtype1 4 9
subtype2 11 7

Figure S27.  Get High-res Image Clustering Approach #7: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #3: 'GENDER'

'MIRseq Mature CNMF subtypes' versus 'RACE'

P value = 0.151 (Fisher's exact test), Q value = 1

Table S35.  Clustering Approach #7: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #4: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 16 1 14
subtype1 9 0 4
subtype2 7 1 10

Figure S28.  Get High-res Image Clustering Approach #7: 'MIRseq Mature CNMF subtypes' versus Clinical Feature #4: 'RACE'

Clustering Approach #8: 'MIRseq Mature cHierClus subtypes'

Table S36.  Description of clustering approach #8: 'MIRseq Mature cHierClus subtypes'

Cluster Labels 1 2 3 4 5 6 7 8
Number of samples 3 4 3 4 8 3 4 2
'MIRseq Mature cHierClus subtypes' versus 'Time to Death'

P value = 0.4 (logrank test), Q value = 1

Table S37.  Clustering Approach #8: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 28 4 0.2 - 211.2 (25.3)
subtype1 3 0 0.8 - 22.3 (4.3)
subtype2 3 0 0.2 - 42.7 (4.3)
subtype3 3 0 15.0 - 196.6 (25.9)
subtype4 4 1 10.3 - 26.0 (13.1)
subtype5 8 1 0.7 - 211.2 (29.2)
subtype6 3 1 35.5 - 106.1 (52.0)
subtype7 4 1 4.6 - 43.9 (27.8)

Figure S29.  Get High-res Image Clustering Approach #8: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #1: 'Time to Death'

'MIRseq Mature cHierClus subtypes' versus 'AGE'

P value = 0.829 (Kruskal-Wallis (anova)), Q value = 1

Table S38.  Clustering Approach #8: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 29 56.9 (12.3)
subtype1 3 61.0 (13.5)
subtype2 4 62.5 (11.6)
subtype3 3 56.7 (14.6)
subtype4 4 58.2 (11.0)
subtype5 8 51.6 (12.1)
subtype6 3 54.7 (23.1)
subtype7 4 59.5 (7.1)

Figure S30.  Get High-res Image Clustering Approach #8: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #2: 'AGE'

'MIRseq Mature cHierClus subtypes' versus 'GENDER'

P value = 0.211 (Fisher's exact test), Q value = 1

Table S39.  Clustering Approach #8: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 14 15
subtype1 2 1
subtype2 2 2
subtype3 0 3
subtype4 1 3
subtype5 4 4
subtype6 1 2
subtype7 4 0

Figure S31.  Get High-res Image Clustering Approach #8: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #3: 'GENDER'

'MIRseq Mature cHierClus subtypes' versus 'RACE'

P value = 0.2 (Fisher's exact test), Q value = 1

Table S40.  Clustering Approach #8: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #4: 'RACE'

nPatients ASIAN WHITE
ALL 16 13
subtype1 2 1
subtype2 1 3
subtype3 1 2
subtype4 4 0
subtype5 6 2
subtype6 1 2
subtype7 1 3

Figure S32.  Get High-res Image Clustering Approach #8: 'MIRseq Mature cHierClus subtypes' versus Clinical Feature #4: 'RACE'

Methods & Data
Input
  • Cluster data file = DLBC-TP.mergedcluster.txt

  • Clinical data file = DLBC-TP.merged_data.txt

  • Number of patients = 35

  • Number of clustering approaches = 8

  • Number of selected clinical features = 4

  • 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

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)
[3] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[4] 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)
[5] 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)