Analysis Overview
Prostate Adenocarcinoma (Primary solid tumor)
17 October 2017  |  None
Maintainer Information
Maintained by Broad Institute GDAC (Broad Institute of MIT & Harvard)
Overview
Introduction

This is an overview of Prostate Adenocarcinoma analysis pipelines from FireCloud run "17 October 2017".

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 FireCloud 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

    • SNP6 Copy number analysis (GISTIC2)
      View Report | There were 495 tumor samples used in this analysis: 40 significant arm-level results, 20 significant focal amplifications, and 28 significant focal deletions were found.

  • Correlations to Clinical Parameters

    • Correlation between copy number variation genes (focal events) and selected clinical features
      View Report | Testing the association between copy number variation 48 focal events and 11 clinical features across 495 patients, 260 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 80 arm-level events and 11 clinical features across 495 patients, 303 significant findings detected with Q value < 0.25.

    • Correlation between mRNAseq expression and clinical features
      View Report | Testing the association between 18723 genes and 11 clinical features across 495 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 8 clinical features related to at least one genes.

  • Clustering Analyses

    • Clustering of copy number data by focal peak region with absolute value: consensus NMF
      View Report | The most robust consensus NMF clustering of 495 samples using the 48 most variable genes was identified for k = 3 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

    • Clustering of copy number data by peak region with threshold value: consensus NMF
      View Report | The most robust consensus NMF clustering of 493 samples using the 48 most variable genes was identified for k = 3 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

    • Clustering of lincRNA expression: consensus hierarchical
      View Report | Median absolute deviation (MAD) was used to select 2500 most variable lincRNAs. Consensus ward linkage hierarchical clustering of 494 samples and 2500 lincRNAs identified 4 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

    • Clustering of lincRNA expression: consensus NMF
      View Report | The most robust consensus NMF clustering of 495 samples using the 2500 most variable lincRNAs was identified for k = 5 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

    • Clustering of miR mature expression: consensus hierarchical
      View Report | Median absolute deviation (MAD) was used to select 262 most variable miRs. Consensus ward linkage hierarchical clustering of 493 samples and 262 miRs identified 4 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

    • Clustering of miR mature expression: consensus NMF
      View Report | The most robust consensus NMF clustering of 494 samples using the 262 most variable miRs was identified for k = 3 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

    • Clustering of protein coding gene expression: consensus NMF
      View Report | The most robust consensus NMF clustering of 495 samples using the 2500 most variable genes was identified for k = 5 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

    • Clustering of Protein-coding gene expression: consensus hierarchical
      View Report | Median absolute deviation (MAD) was used to select 2500 most variable genes. Consensus ward linkage hierarchical clustering of 494 samples and 2500 genes identified 7 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

  • Other Analyses

    • Identification of putative miR direct targets by sequencing data
      View Report | The CLR algorithm was applied on 688 miRs and 18723 mRNAs across 491 samples. After 2 filtering steps, the number of 189 miR:gene pairs were detected.

    • Methylation__HM450_Clustering_CNMF
      View Report | The most robust consensus NMF clustering of 497 samples using the 4912 most variable genes was identified for k = 6 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

    • Methylation__HM450_Clustering_Consensus_Plus
      View Report | Median absolute deviation (MAD) was used to select 2500 most variable genes. Consensus ward linkage hierarchical clustering of 496 samples and 2500 genes identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

  • Other Correlation Analyses

    • Correlation between copy number variation genes (focal events) and molecular subtypes
      View Report | Testing the association between copy number variation 48 focal events and 10 molecular subtypes across 495 patients, 351 significant findings detected with P value < 0.05 and 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 80 arm-level events and 10 molecular subtypes across 495 patients, 345 significant findings detected with P value < 0.05 and Q value < 0.25.

Methods & Data
Input

  • Summary Report Date = Thu Dec 14 14:05:42 2017

  • Protection = FALSE

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