Analysis Overview for Skin Cutaneous Melanoma
(All_Samples 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 "02 May 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 288 tumor samples used in this analysis: 23 significant arm-level results, 22 significant focal amplifications, and 29 significant focal deletions were found.

    • Mutation Analysis (MutSig v1.5)
      View Report | 

    • Mutation Analysis (MutSig v2.0)
      View Report | 

    • Mutation Analysis (MutSigCV v0.9)
      View Report | 

  • Clustering Analyses

    • Clustering of copy number data by focal peak region with log2 ratio: consensus NMF
      View Report | The most robust consensus NMF clustering of 288 samples using the 51 copy number focal regions was identified for k = 4 clusters. We computed the clustering for k = 2 to k = 8 and used the cophenetic correlation coefficient to determine the best solution.

    • Clustering of Methylation: consensus NMF
      View Report | The 10877 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 316 samples and 10877 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.

    • Clustering of RPPA data: consensus NMF
      View Report | The most robust consensus NMF clustering of 162 samples using the 175 most variable proteins 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 RPPA data: consensus hierarchical
      View Report | The 175 most variable proteins were selected. Consensus average linkage hierarchical clustering of 162 samples and 175 proteins 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 mRNAseq gene expression: consensus NMF
      View Report | The most robust consensus NMF clustering of 282 samples using the 1500 most variable genes was identified for k = 4 clusters. We computed the clustering for k = 2 to k = 8 and used the cophenetic correlation coefficient to determine the best solution.

    • Clustering of mRNAseq gene expression: consensus hierarchical
      View Report | The 1500 most variable genes were selected. Consensus average linkage hierarchical clustering of 282 samples and 1500 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.

    • Clustering of miRseq precursor expression: consensus NMF
      View Report | We filtered the data to 150 most variable miRs. Consensus NMF clustering of 282 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 precursor expression: consensus hierarchical
      View Report | We filtered the data to 150 most variable miRs. Consensus average linkage hierarchical clustering of 282 samples and 150 miRs identified 2 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

    • Preprocessing of clinical data
      View Report | Clinical data for tier 1 clinical variables are generated.

    • Correlation between copy number variations of arm-level result and selected clinical features
      View Report | Testing the association between copy number variation 77 arm-level results and 9 clinical features across 202 patients, one significant finding detected with Q value < 0.25.

    • Correlation between copy number variations of arm-level result and selected clinical features
      View Report | Testing the association between copy number variation 77 arm-level results and 9 clinical features across 202 patients, one significant finding detected with Q value < 0.25.

    • Correlation between copy number variation genes (focal) and selected clinical features
      View Report | Testing the association between copy number variation 51 arm-level results and 9 clinical features across 202 patients, no significant finding detected with Q value < 0.25.

    • Correlation between copy number variation genes (focal) and selected clinical features
      View Report | Testing the association between copy number variation 51 arm-level results and 9 clinical features across 202 patients, one significant finding detected with Q value < 0.25.

    • Correlation between gene methylation status and clinical features
      View Report | Testing the association between 17134 genes and 8 clinical features across 195 samples, statistically thresholded by Q value < 0.05, 8 clinical features related to at least one genes.

    • Correlation between gene methylation status and clinical features
      View Report | Testing the association between 17134 genes and 8 clinical features across 195 samples, statistically thresholded by Q value < 0.05, 7 clinical features related to at least one genes.

    • Correlation between molecular cancer subtypes and selected clinical features
      View Report | Testing the association between subtypes identified by 8 different clustering approaches and 9 clinical features across 211 patients, 6 significant findings detected with P value < 0.05 and Q value < 0.25.

    • Correlation between molecular cancer subtypes and selected clinical features
      View Report | Testing the association between subtypes identified by 8 different clustering approaches and 9 clinical features across 211 patients, 6 significant findings detected with P value < 0.05 and Q value < 0.25.

    • Correlation between gene mutation status and selected clinical features
      View Report | Testing the association between mutation status of 106 genes and 9 clinical features across 184 patients, 9 significant findings detected with Q value < 0.25.

    • Correlation between RPPA expression and clinical features
      View Report | Testing the association between 175 genes and 8 clinical features across 121 samples, statistically thresholded by Q value < 0.05, 3 clinical features related to at least one genes.

    • Correlation between RPPA expression and clinical features
      View Report | Testing the association between 175 genes and 8 clinical features across 121 samples, statistically thresholded by Q value < 0.05, 3 clinical features related to at least one genes.

    • Correlation between mRNAseq expression and clinical features
      View Report | Testing the association between 18094 genes and 8 clinical features across 198 samples, statistically thresholded by Q value < 0.05, 8 clinical features related to at least one genes.

    • Correlation between mRNAseq expression and clinical features
      View Report | Testing the association between 18094 genes and 8 clinical features across 198 samples, statistically thresholded by Q value < 0.05, 8 clinical features related to at least one genes.

    • Correlation between miRseq expression and clinical features
      View Report | Testing the association between 598 genes and 8 clinical features across 197 samples, statistically thresholded by Q value < 0.05, 3 clinical features related to at least one genes.

    • Correlation between miRseq expression and clinical features
      View Report | Testing the association between 598 genes and 8 clinical features across 197 samples, statistically thresholded by Q value < 0.05, 3 clinical features related to at least one genes.

    • Correlations between copy number and mRNAseq expression
      View Report | The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are 981.3, 1653, 2185, 2755, 3360, 4020.8, 4639, 5327, 6085.7, respectively.

    • Correlation between mRNA expression and DNA methylation
      View Report | The top 25 correlated methylation probes per gene are displayed. Total number of matched samples = 282. Number of gene expression samples = 282. Number of methylation samples = 282.

    • Correlation between copy number variations of arm-level result and molecular subtypes
      View Report | Testing the association between copy number variation 78 arm-level results and 8 molecular subtypes across 288 patients, 44 significant findings 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 51 peak regions and 8 molecular subtypes across 288 patients, 46 significant findings detected with Q value < 0.25.

    • Correlation between gene mutation status and molecular subtypes
      View Report | Testing the association between mutation status of 109 genes and 8 molecular subtypes across 264 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.

  • Pathway Analyses

    • PARADIGM pathway analysis of mRNASeq expression data
      View Report | There were 61 significant pathways identified in this analysis.

    • PARADIGM pathway analysis of mRNASeq expression and copy number data
      View Report | There were 64 significant pathways identified in this analysis.

Methods & Data
Input

  • Run Prefix = awg_skcm__2013_05_02

  • Summary Report Date = Mon May 13 16:18:51 2013

  • Protection = FALSE

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