Clustering of mRNAseq gene expression: consensus NMF
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
28 January 2016
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analyses__2016_01_28
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
(2016):
Clustering of mRNAseq gene expression: consensus NMF.
Broad Institute of MIT and Harvard.
doi:10.7908/C1MP52P7
Overview
Introduction
Summary
The most robust consensus NMF clustering of 290 samples using the 1500 most variable genes was identified for k = 5 clusters. We computed the clustering for k = 2 to k = 10 and uused the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.
Results
Gene expression patterns of molecular subtypes
Silhouette widths, Cophenetic Correlation Coefficients and Consensus matrix
Samples assignment with silhouette width
Marker genes of each subtype
Methods & Data
Copyright © 2016
Broad Institute TCGA GDAC as part of the TCGA Research Network.
All rights reserved.