Clustering of mRNA expression: consensus NMF
Rectum Adenocarcinoma (Primary solid tumor)
17 October 2014
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analyses__2014_10_17
Maintainer Information
Citation Information
Maintained by Hailei Zhang
(Broad Institute)
Cite as
Broad Institute TCGA Genome Data Analysis Center
(2014):
Clustering of mRNA expression: consensus NMF.
Broad Institute of MIT and Harvard.
doi:10.7908/C1T43S10
Overview
Introduction
Summary
The most robust consensus NMF clustering of 69 samples using the 1500 most variable genes was identified for k = 3 clusters. We computed the clustering for k = 2 to k = 8 and used the cophenetic correlation coefficient to determine the best solution.
Results
Gene expression patterns of molecular subtypes
Consensus and correlation matrix
Silhouette widths
Samples assignment with silhouette width
Marker genes of each subtype
Methods & Data
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Broad Institute TCGA GDAC as part of the TCGA Research Network.
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