Analysis Overview for Liver Hepatocellular Carcinoma

Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)

Overview

Introduction

This is the analysis overview for Firehose run "24 October 2012".

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 11633 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 98 samples and 11633 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.
Clustering of miRseq expression: consensus NMF
View Report | We filtered the data to 150 most variable miRs. Consensus NMF clustering of 96 samples and 150 miRs 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.
Clustering of miRseq expression: consensus hierarchical
View Report | We filtered the data to 150 most variable miRs. Consensus average linkage hierarchical clustering of 96 samples and 150 miRs 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.

Correlation Analyses

Correlation between molecular cancer subtypes and selected clinical features
View Report | Testing the association between subtypes identified by 3 different clustering approaches and 3 clinical features across 62 patients, one significant finding detected with P value < 0.05.
Correlation between miRseq expression and clinical features
View Report | Testing the association between 570 genes and 3 clinical features across 61 samples, statistically thresholded by Q value < 0.05, no clinical feature related to at least one genes.

Methods & Data

Input

Run Prefix = analyses__2012_10_24
Summary Report Date = Fri Nov 16 16:09:10 2012
Protection = FALSE

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