Clustering of Methylation: consensus NMF
Testicular Germ Cell Tumors (Primary solid tumor)
21 August 2015
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analyses__2015_08_21
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
(2015):
Clustering of Methylation: consensus NMF.
Broad Institute of MIT and Harvard.
doi:10.7908/C1JH3KGN
Overview
Introduction
Summary
The 15917 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 150 samples and 15917 genes identified 3 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
Marker genes of each subtype
Methods & Data
Copyright © 2015
Broad Institute TCGA GDAC as part of the TCGA Research Network.
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