Clustering of Methylation: consensus NMF
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
23 May 2013
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analyses__2013_05_23
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
(2013):
Clustering of Methylation: consensus NMF.
Broad Institute of MIT and Harvard.
doi:10.7908/C1S75DDV
Overview
Introduction
Summary
The 2419 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 582 samples and 2419 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 © 2013
Broad Institute TCGA GDAC as part of the TCGA Research Network.
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