Clustering of Methylation: consensus NMF

Breast Invasive Carcinoma (Primary solid tumor)

15 January 2014 | analyses__2014_01_15

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): Clustering of Methylation: consensus NMF. Broad Institute of MIT and Harvard. doi:10.7908/C1J101KD

- Overview

+ Introduction

- Summary

The 5015 most variable methylated genes were selected based on variation. The variation cutoff are set for each tumor type empirically by fitting a bimodal distriution. For genes with multiple methylation probes, we chose the most variable one to represent the gene. Consensus NMF clustering of 711 samples and 5015 genes identified 6 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

- Results

+ Silhouette width of each sample in robust cluster

+ Gene methylation patterns of molecular subtype

+ Consensus and correlation matrix

+ Samples assignment with silhouette width

SampleName	cluster	silhouetteValue
TCGA-A1-A0SB-01	1	0.18
TCGA-A1-A0SK-01	1	0.23
TCGA-A1-A0SO-01	1	0.23
TCGA-A1-A0SP-01	1	0.21
TCGA-A2-A0SX-01	1	0.14
TCGA-A2-A0T0-01	1	0.25
TCGA-A2-A0T2-01	1	0.32
TCGA-A2-A0YE-01	1	0.26
TCGA-A2-A0YJ-01	1	0.31
TCGA-A2-A0YM-01	1	0.31

SampleName	K=2	K=3	K=4	K=5	K=6	K=7	K=8
TCGA-A1-A0SB-01	1	1	1	1	1	1	1
TCGA-A1-A0SH-01	1	2	2	2	2	2	3
TCGA-A1-A0SK-01	1	1	1	1	1	1	1
TCGA-A1-A0SO-01	1	1	1	1	1	1	1
TCGA-A1-A0SP-01	1	1	1	1	1	1	1
TCGA-A2-A0CR-01	1	1	1	5	6	6	6
TCGA-A2-A0EN-01	1	2	1	5	6	6	6
TCGA-A2-A0EP-01	1	1	1	5	6	6	6
TCGA-A2-A0ST-01	1	1	1	5	6	6	6
TCGA-A2-A0SU-01	1	2	2	4	5	5	3

+ Marker genes of each subtype

Composite.Element.REF	p	difference	q	subclass
CAPN2	6.2e-141	0.56	3.1e-137	1
LOC440335	1.7e-64	0.5	3.4e-63	1
SEPT12	1.7e-64	0.5	3.4e-63	1
PGCP	1.3e-63	0.49	2.4e-62	1
GPR37L1	1.1e-57	0.49	1.5e-56	1
SH3PXD2B	3.7e-101	0.47	3.9e-99	1
E4F1	4e-87	0.47	2.3e-85	1
FOXA1	5.8e-35	0.47	3e-34	1
MITF	7e-84	0.47	3.5e-82	1
PPFIA3	9.4e-35	0.46	4.9e-34	1

+ Methods & Data

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