Analysis Overview for Head and Neck Squamous Cell 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 January 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

- Sequence and Copy Number Analyses

- Copy number analysis (GISTIC2)
  View Report | There were 165 tumor samples used in this analysis: 20 significant arm-level results, 30 significant focal amplifications, and 45 significant focal deletions were found.

- Other Analyses

- Clustering of miRseq expression: consensus NMF
  View Report | We filtered the data to 150 most variable miRs. Consensus NMF clustering of 89 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 89 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.

- Paradigm Report
  View Report | There were 131 significant pathways identified in this analysis.

Methods & Data
Input

- Firehose Directory = /xchip/cga1/tcga_gdac_firehose_output

- Run Prefix = prod__2012_01_24

- Summary Report Date = Fri Feb 24 12:57:32 2012

- Protection = FALSE

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