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

This is the analysis overview for Firehose run "25 August 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 161 tumor samples used in this analysis: 21 significant arm-level results, 29 significant focal amplifications, and 39 significant focal deletions were found.

    • Mutation Analysis (MutSig)
      View Report | MAF used for this analysis: STAD.final_analysis_set.maf

  • Clustering Analyses

    • Clustering of copy number data: consensus NMF
      View Report | The most robust consensus NMF clustering of 161 samples using the 68 copy number focal regions was identified for k = 5 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 5816 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 69 samples and 5816 genes identified 4 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 57 samples using the 1500 most variable genes was identified for k = 6 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 57 samples and 1500 genes identified 4 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 expression: consensus NMF
      View Report | We filtered the data to 150 most variable miRs. Consensus NMF clustering of 151 samples and 150 miRs identified 5 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 expression: consensus hierarchical
      View Report | We filtered the data to 150 most variable miRs. Consensus average linkage hierarchical clustering of 151 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 copy number variations of arm-level result and selected clinical features
      View Report | Testing the association between copy number variation 73 arm-level results and 10 clinical features across 158 patients, one significant finding detected with Q value < 0.25.

    • Correlation between copy number variation genes and selected clinical features
      View Report | Testing the association between copy number variation of 68 peak regions and 10 clinical features across 158 patients, no significant finding detected with Q value < 0.25.

    • Correlation between gene methylation status and clinical features
      View Report | Testing the association between 20229 genes and 9 clinical features across 68 samples, statistically thresholded by Q value < 0.05, 4 clinical features related to at least one genes.

    • Correlation between gene mutation status and selected clinical features
      View Report | Testing the association between mutation status of 137 genes and 9 clinical features across 132 patients, one significant finding detected with Q value < 0.25.

    • Correlation between mRNAseq expression and clinical features
      View Report | Testing the association between 19446 genes and 8 clinical features across 57 samples, statistically thresholded by Q value < 0.05, 4 clinical features related to at least one genes.

    • Correlation between miRseq expression and clinical features
      View Report | Testing the association between 533 genes and 10 clinical features across 150 samples, statistically thresholded by Q value < 0.05, 5 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 1101.4, 2198, 2918, 3601, 4282, 4997.4, 5705.8, 6477.2, 7348, 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 = 0. Number of gene expression samples = 57. Number of methylation samples = 69.

Methods & Data
Input

  • Run Prefix = analyses__2012_08_25

  • Summary Report Date = Thu Sep 27 12:11:45 2012

  • Protection = FALSE

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