Stomach Adenocarcinoma: Clustering of Methylation: consensus NMF
(primary solid tumor cohort)
(primary solid tumor cohort)
Maintained by TCGA GDAC Team
(Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction
Summary
The 6176 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 146 samples and 6176 genes identified 4 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.
All rights reserved.