Analysis Overview - Uveal Melanoma (Primary solid tumor)

Analysis Overview

Uveal Melanoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

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 (2014): Analysis Overview for Uveal Melanoma (Primary solid tumor cohort) - 15 July 2014. Broad Institute of MIT and Harvard. doi:10.7908/C1JD4VM3

Overview

Introduction

This is an overview of Uveal Melanoma analysis pipelines from Firehose run "15 July 2014".

Summary

Note: These results are offered to the community as an additional reference point, enabling a wide range of cancer biologists, clinical investigators, and genome and computational scientists to easily incorporate TCGA into the backdrop of ongoing research. While every effort is made to ensure that Firehose input data and algorithms are of the highest possible quality, these analyses have not been reviewed by domain experts.

Results

Clustering Analyses

Clustering of Methylation: consensus NMF
View Report | The 7972 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 80 samples and 7972 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.

Methods & Data

Input

Summary Report Date = Tue Sep 16 19:10:43 2014
Protection = FALSE

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