Analysis Overview for PANCANCER cohort with 12 disease types
(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 "16 January 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 4791 tumor samples used in this analysis: 33 significant arm-level results, 40 significant focal amplifications, and 50 significant focal deletions were found.

- Clustering Analyses

- Clustering of mRNA expression: consensus NMF
  View Report | The most robust consensus NMF clustering of 1604 samples using the 1500 most variable genes was identified for k = 3 clusters. We computed the clustering for k = 2 to k = 8 and used the cophenetic correlation coefficient to determine the best solution.

- Clustering of miR expression: consensus NMF
  View Report | We filtered the data to 150 most variable miRs. Consensus NMF clustering of 568 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 568 samples and 150 miRs identified 6 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 15521 genes and 13 clinical features across 238 samples, statistically thresholded by Q value < 0.05, 6 clinical features related to at least one genes.

- Correlation between mRNA expression and clinical features
  View Report | Testing the association between 17814 genes and 15 clinical features across 1596 samples, statistically thresholded by Q value < 0.05, 14 clinical features related to at least one genes.

- Correlation between miR expression and clinical features
  View Report | Testing the association between 817 miRs and 6 clinical features across 560 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 = 238. Number of gene expression samples = 1604. Number of methylation samples = 238.

- Other Analyses

- The boxplot mRNA array based expression data
  View Report

- 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__2013_01_16

- Summary Report Date = Mon Feb 11 18:12:21 2013

- Protection = FALSE

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