Analysis Overview for Lung 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 "21 March 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 205 tumor samples used in this analysis: 23 significant arm-level results, 19 significant focal amplifications, and 32 significant focal deletions were found.

    • Mutation Analysis (MutSig)
      View Report | Significantly mutated genes (q ≤ 0.1): 90

  • Clustering Analyses

    • Clustering of mRNA expression: consensus NMF
      View Report | The most robust consensus NMF clustering of 32 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 mRNA expression: consensus hierarchical
      View Report | The 1500 most variable genes were selected. Consensus average linkage hierarchical clustering of 32 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 mRNAseq gene expression: consensus NMF
      View Report | The most robust consensus NMF clustering of 106 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 106 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 Methylation: consensus NMF
      View Report | The 254 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 127 samples and 254 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 95 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 expression: consensus hierarchical
      View Report | We filtered the data to 150 most variable miRs. Consensus average linkage hierarchical clustering of 95 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

    • Correlations between copy number and mRNA expression
      View Report | The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are -0.11866, -0.0159, 0.0651, 0.13574, 0.2039, 0.2728, 0.34674, 0.4259, 0.53034, respectively.

    • Correlation between mRNA expression and DNA methylation
      View Report | The top 25 correlated methylation probe(s) per gene are displayed. Total number of matched samples = 31 Number of gene expression samples = 129 Number of methylation samples = 32

  • Other Analyses

    • PARADIGM pathway analysis of mRNA expression data
      View Report | There were 44 significant pathways identified in this analysis.

    • Association of mutation, copy number alteration, and subtype markers with pathways
      View Report | There are 90 genes with significant mutation (Q value <= 0.1) and 380 genes with significant copy number alteration (Q value <= 0.25). The identified marker genes (Q value <= 0.01 or within top 2000) are 39 for subtype 1, 39 for subtype 2, 39 for subtype 3. Pathways significantly enriched with these genes (Q value <= 0.01) are identified :

Methods & Data
Input

  • Firehose Directory = /xchip/cga1/tcga_gdac_firehose_output

  • Run Prefix = analyses__2012_03_21

  • Summary Report Date = Fri Apr 20 10:52:59 2012

  • Protection = FALSE

Copyright © 2011 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
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