Clustering of Methylation: consensus NMF
Breast Invasive Carcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_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 (2013): Breast Invasive Carcinoma (Primary solid tumor cohort) - 21 April 2013: Clustering of Methylation: consensus NMF. Broad Institute of MIT and Harvard. doi:10.7908/C1TB14TR
- Overview
+ Introduction
- Summary

The 4836 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 615 samples and 4836 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
+ Marker genes of each subtype
+ Methods & Data