Analysis Overview for Esophageal Carcinoma
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

This is the analysis overview for Firehose run "26 March 2013".

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 20 tumor samples used in this analysis: 9 significant arm-level results, 14 significant focal amplifications, and 16 significant focal deletions were found.

- Clustering Analyses

- Clustering of Methylation: consensus NMF
  View Report | The 9036 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 50 samples and 9036 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.

- Correlation Analyses

- Correlation between copy number variations of arm-level result and molecular subtypes
  View Report | Testing the association between copy number variation 38 arm-level results and molecular subtype 'METHLYATION_CNMF' across 20 patients, no significant finding detected with Q value < 0.25.

- Correlation between copy number variation genes and molecular subtypes
  View Report | Testing the association between copy number variation of 27 peak regions and molecular subtype 'METHLYATION_CNMF' across 20 patients, one significant finding detected with Q value < 0.25.

Methods & Data
Input

- Run Prefix = analyses__2013_03_26

- Summary Report Date = Sat Apr 20 08:16:37 2013

- Protection = FALSE

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