Analysis Overview for PANCANCER subset with 8 initial disease types
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
Overview
Introduction

This is the analysis overview for Firehose run "13 September 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 3770 tumor samples used in this analysis: 32 significant arm-level results, 39 significant focal amplifications, and 50 significant focal deletions were found.

- Clustering Analyses

- Clustering of miR expression: consensus NMF
  View Report | We filtered the data to 150 most variable miRs. Consensus NMF clustering of 570 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 miR expression: consensus hierarchical
  View Report | We filtered the data to 150 most variable miRs. Consensus average linkage hierarchical clustering of 570 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.

- Correlation Analyses

- Correlation between gene methylation status and clinical features
  View Report | Testing the association between 15549 genes and 10 clinical features across 237 samples, statistically thresholded by Q value < 0.05, 7 clinical features related to at least one genes.

- Correlation between mRNA expression and clinical features
  View Report | Testing the association between 17814 genes and 12 clinical features across 1569 samples, statistically thresholded by Q value < 0.05, 12 clinical features related to at least one genes.

- Correlation between miR expression and clinical features
  View Report | Testing the association between 817 miRs and 7 clinical features across 562 samples, statistically thresholded by Q value < 0.05, 3 clinical features related to at least one miRs.

- Correlation between mRNA expression and DNA methylation
  View Report | The top 25 correlated methylation probes per gene are displayed. Total number of matched samples = 239. Number of gene expression samples = 1577. Number of methylation samples = 1786.

- Other Analyses

- Identification of putative miR direct targets
  View Report | This pipeline use a relevance network approach to infer putative miR:mRNA regulatory connections. All miR:mRNA pairs that have correlations < -0.3 and have predicted interactions in three sequence prediction databases (Miranda, Pictar, Targetscan) define the final network.

Methods & Data
Input

- Run Prefix = analyses__2012_09_13

- Summary Report Date = Mon Oct 29 23:10:21 2012

- Protection = FALSE

Copyright © 2012 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
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