Analysis Overview
Thyroid Adenocarcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1KK9927
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Analysis Overview for Thyroid Adenocarcinoma (Primary solid tumor cohort) - 22 February 2013. Broad Institute of MIT and Harvard. doi:10.7908/C1KK9927
Overview
Introduction

This is an overview of Thyroid Adenocarcinoma analysis pipelines from Firehose run "22 February 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 430 tumor samples used in this analysis: 18 significant arm-level results, 0 significant focal amplifications, and 31 significant focal deletions were found.

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

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

    • Mutation Analysis (MutSig vS2N)
      View Report | 

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

  • Correlations to Clinical Parameters

    • Correlation between copy number variation genes (focal) and selected clinical features
      View Report | Testing the association between copy number variation 24 arm-level results and 15 clinical features across 284 patients, 15 significant findings 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 36 arm-level results and 15 clinical features across 284 patients, 27 significant findings detected with Q value < 0.25.

    • Correlation between gene methylation status and clinical features
      View Report | Testing the association between 17090 genes and 13 clinical features across 268 samples, statistically thresholded by Q value < 0.05, 11 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 23 genes and 14 clinical features across 229 patients, 6 significant findings detected with Q value < 0.25.

    • Correlation between miRseq expression and clinical features
      View Report | Testing the association between 532 genes and 13 clinical features across 282 samples, statistically thresholded by Q value < 0.05, 10 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 10 different clustering approaches and 15 clinical features across 288 patients, 34 significant findings detected with P value < 0.05 and Q value < 0.25.

    • Correlation between mRNAseq expression and clinical features
      View Report | Testing the association between 18025 genes and 13 clinical features across 271 samples, statistically thresholded by Q value < 0.05, 13 clinical features related to at least one genes.

    • Correlation between RPPA expression and clinical features
      View Report | Testing the association between 175 genes and 13 clinical features across 163 samples, statistically thresholded by Q value < 0.05, 8 clinical features related to at least one genes.

  • 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 430 samples using the 31 copy number focal regions 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 Methylation: consensus NMF
      View Report | The 5108 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 435 samples and 5108 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 mature expression: consensus hierarchical
      View Report | We filtered the data to 164 most variable miRs. Consensus average linkage hierarchical clustering of 411 samples and 164 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 mature expression: consensus NMF
      View Report | We filtered the data to 164 most variable miRs. Consensus NMF clustering of 411 samples and 164 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 411 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 NMF
      View Report | We filtered the data to 150 most variable miRs. Consensus NMF clustering of 411 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 mRNAseq gene expression: consensus hierarchical
      View Report | The 1500 most variable genes were selected. Consensus average linkage hierarchical clustering of 409 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 409 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 RPPA data: consensus hierarchical
      View Report | The 175 most variable proteins were selected. Consensus average linkage hierarchical clustering of 224 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 RPPA data: consensus NMF
      View Report | The most robust consensus NMF clustering of 224 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.

  • Other Analyses

    • Correlate_Clinical_vs_CustomEvents
      View Report | Testing the association between mutation status of 6 genes and 14 clinical features across 229 patients, 3 significant findings detected with P value < 0.05 and Q value < 0.25.

    • Correlate_Clinical_vs_Molecular_Signatures
      View Report | Testing the association between subtypes identified by 10 different clustering approaches and 15 clinical features across 288 patients, 34 significant findings detected with P value < 0.05 and Q value < 0.25.

  • Pathway Analyses

    • HotNet pathway analysis of mutation and copy number data
      View Report

    • PARADIGM pathway analysis of mRNASeq expression and copy number data
      View Report | There were 39 significant pathways identified in this analysis.

    • PARADIGM pathway analysis of mRNASeq expression data
      View Report | There were 48 significant pathways identified in this analysis.

  • Other Correlation Analyses

    • Correlation between copy number variation genes and molecular subtypes
      View Report | Testing the association between copy number variation of 25 peak regions and 8 molecular subtypes across 430 patients, 44 significant findings detected with Q value < 0.25.

    • Correlation between copy number variations of arm-level result and molecular subtypes
      View Report | Testing the association between copy number variation 42 arm-level results and 8 molecular subtypes across 430 patients, 94 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 41 genes and 8 molecular subtypes across 323 patients, 20 significant findings detected with P value < 0.05 and Q value < 0.25.

    • Correlation between mRNA expression and DNA methylation
      View Report | The top 25 correlated methylation probes per gene are displayed. Total number of matched samples = 409. Number of gene expression samples = 409. Number of methylation samples = 409.

    • Correlations between copy number and mRNAseq expression
      View Report | The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are 428, 1141, 1804, 2135, 2457, 2808, 3205, 3706.4, 4367.2, respectively.

Methods & Data
Input

  • Summary Report Date = Mon Aug 5 20:58:23 2013

  • Protection = FALSE

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