Analysis Overview for Kidney Chromophobe
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)

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


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.

  • Sequence and Copy Number Analyses

    • Copy number analysis (GISTIC2)
      View Report | There were 65 tumor samples used in this analysis: 14 significant arm-level results, 2 significant focal amplifications, and 0 significant focal deletions were found.

  • Clustering Analyses

    • Clustering of Methylation: consensus NMF
      View Report | The 13329 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 65 samples and 13329 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.

Methods & Data
  • Run Prefix = analyses__2012_10_24

  • Summary Report Date = Fri Nov 16 16:03:12 2012

  • Protection = FALSE