Analysis Overview for Lung Squamous Cell Carcinoma
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 May 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 282 tumor samples used in this analysis: 28 significant arm-level results, 31 significant focal amplifications, and 42 significant focal deletions were found.

  • Clustering Analyses

    • Clustering of mRNA expression: consensus NMF
      View Report | The most robust consensus NMF clustering of 154 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 154 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 223 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 223 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 Methylation: consensus NMF
      View Report | The 382 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 133 samples and 382 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 202 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 202 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 -0.0231, 0.0444, 0.10392, 0.17168, 0.2449, 0.3225, 0.40244, 0.4808, 0.56878, 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 = 133 Number of gene expression samples = 135 Number of methylation samples = 154

  • Other Analyses

    • Correlation between mRNA expression and clinical features
      View Report | Testing the association between 17814 genes and 9 clinical features across 154 samples, statistically thresholded by Q value < 0.05, 4 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 7 different clustering approaches and 10 clinical features across 229 patients, 14 significant findings detected with P value < 0.05.

    • Correlation between gene mutation status and selected clinical features
      View Report | Testing the association between mutation status of 551 genes and 10 clinical features across 178 patients, no significant finding detected with Q value < 0.25.

    • Correlations between copy number and mRNAseq expression
      View Report | The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are 1104.8, 1780, 2368.4, 2973.2, 3605, 4290, 4957, 5614, 6318.2, respectively.

    • Association of mutation, copy number alteration, and subtype markers with pathways
      View Report | There are 344 genes with significant mutation (Q value <= 0.1) and 228 genes with significant copy number alteration (Q value <= 0.25). The identified marker genes (Q value <= 0.01 or within top 2000) are 1580 for subtype 1, 1580 for subtype 2, 1580 for subtype 3. Pathways significantly enriched with these genes (Q value <= 0.01) are identified :

    • PARADIGM pathway analysis of mRNA expression data
      View Report | There were 59 significant pathways identified in this analysis.

    • PARADIGM pathway analysis of mRNA expression and copy number data
      View Report | There were 42 significant pathways identified in this analysis.

Methods & Data
Input

  • Firehose Directory = /local/cga-fh/tcga-gdac

  • Run Prefix = analyses__2012_05_25

  • Summary Report Date = Sat Jun 16 13:15:35 2012

  • Protection = FALSE

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