Analysis Overview
Prostate Adenocarcinoma (Primary solid tumor)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1794320
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 Prostate Adenocarcinoma (Primary solid tumor cohort) - 23 September 2013. Broad Institute of MIT and Harvard. doi:10.7908/C1794320
Overview
Introduction

This is an overview of Prostate Adenocarcinoma analysis pipelines from Firehose run "23 September 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

- CHASM (Cancer-Specific High-throughput Annotation of Somatic Mutations)
  View Report | There are 6604 mutations identified by MuTect and 478 mutations with significant functional impact at BHFDR <= 0.25.

- LowPass Copy number analysis (GISTIC2)
  View Report | There were 15 tumor samples used in this analysis: 10 significant arm-level results, 1 significant focal amplifications, and 3 significant focal deletions were found.

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

- Mutation Analysis (MutSig v2.0 and MutSigCV v0.9 merged result)
  View Report |

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

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

- Mutation Assessor
  View Report |

- SNP6 Copy number analysis (GISTIC2)
  View Report | There were 197 tumor samples used in this analysis: 17 significant arm-level results, 21 significant focal amplifications, and 25 significant focal deletions were found.

- Correlations to Clinical Parameters

- Correlation between aggregated molecular cancer subtypes and selected clinical features
  View Report | Testing the association between subtypes identified by 10 different clustering approaches and 6 clinical features across 165 patients, 5 significant findings detected with P value < 0.05 and Q value < 0.25.

- Correlation between copy number variation genes (focal events) and selected clinical features
  View Report | Testing the association between copy number variation 46 focal events and 6 clinical features across 160 patients, 4 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 50 arm-level events and 6 clinical features across 160 patients, no significant finding detected with Q value < 0.25.

- Correlation between gene methylation status and clinical features
  View Report | Testing the association between 20008 genes and 5 clinical features across 162 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 470 genes and 5 clinical features across 164 samples, statistically thresholded by Q value < 0.05, 2 clinical features related to at least one genes.

- Correlation between mRNAseq expression and clinical features
  View Report | Testing the association between 18239 genes and 5 clinical features across 161 samples, statistically thresholded by Q value < 0.05, 4 clinical features related to at least one genes.

- Correlation between RPPA expression and clinical features
  View Report | Testing the association between 189 genes and 5 clinical features across 137 samples, statistically thresholded by Q value < 0.05, 1 clinical feature 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 197 samples using the 46 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 3276 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 248 samples and 3276 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 239 most variable miRs. Consensus average linkage hierarchical clustering of 232 samples and 239 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 239 most variable miRs. Consensus NMF clustering of 232 samples and 239 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 precursor expression: consensus hierarchical
  View Report | We filtered the data to 150 most variable miRs. Consensus average linkage hierarchical clustering of 232 samples and 150 miRs 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 precursor expression: consensus NMF
  View Report | We filtered the data to 150 most variable miRs. Consensus NMF clustering of 232 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 mRNAseq gene expression: consensus hierarchical
  View Report | The 1500 most variable genes were selected. Consensus average linkage hierarchical clustering of 195 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 195 samples using the 1500 most variable genes 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 | 189 proteins were selected. Consensus average linkage hierarchical clustering of 164 samples and 189 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 164 samples using 189 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.

- Pathway Analyses

- HotNet pathway analysis of mutation and copy number data
  View Report | There were 3 significant subnetworks identified in HotNet analysis.

- PARADIGM pathway analysis of mRNASeq expression and copy number data
  View Report | There were 44 significant pathways identified in this analysis.

- PARADIGM pathway analysis of mRNASeq expression data
  View Report | There were 42 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 46 peak regions and 10 molecular subtypes across 197 patients, 61 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 32 arm-level results and 10 molecular subtypes across 197 patients, 23 significant findings detected with 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 = 195. Number of gene expression samples = 195. Number of methylation samples = 248.

- Correlations between copy number and mRNAseq expression
  View Report | The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are 688, 1610, 2046, 2475, 2900, 3388, 3950.6, 4629.4, 5461.2, respectively.

Methods & Data
Input

- Summary Report Date = Mon Oct 21 15:24:31 2013

- Protection = FALSE

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