Analysis Overview
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1125S2C
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Analysis Overview for Kidney Renal Clear Cell Carcinoma (Primary solid tumor cohort) - 28 January 2016. Broad Institute of MIT and Harvard. doi:10.7908/C1125S2C
Overview
Introduction

This is an overview of Kidney Renal Clear Cell Carcinoma analysis pipelines from Firehose run "28 January 2016".

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

    • Analysis of mutagenesis by APOBEC cytidine deaminases (P-MACD).
      View Report | There are 476 tumor samples in this analysis. The Benjamini-Hochberg-corrected p-value for enrichment of the APOBEC mutation signature in 0 samples is <=0.05. Out of these, 0 have enrichment values >2, which implies that in such samples at least 50% of APOBEC signature mutations have been in fact made by APOBEC enzyme(s).

    • CHASM 1.0.5 (Cancer-Specific High-throughput Annotation of Somatic Mutations)
      View Report | There are 14607 mutations identified by MuTect and 1154 mutations with significant functional impact at BHFDR <= 0.25.

    • Mutation Analysis (MutSig 2CV v3.1)
      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 528 tumor samples used in this analysis: 28 significant arm-level results, 10 significant focal amplifications, and 19 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 12 different clustering approaches and 12 clinical features across 537 patients, 71 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 29 focal events and 12 clinical features across 528 patients, 73 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 12 clinical features across 528 patients, 127 significant findings detected with Q value < 0.25.

    • Correlation between gene methylation status and clinical features
      View Report | Testing the association between 17087 genes and 12 clinical features across 319 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 10 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 25 genes and 12 clinical features across 436 patients, no significant finding detected with Q value < 0.25.

    • Correlation between miRseq expression and clinical features
      View Report | Testing the association between 460 miRs and 12 clinical features across 516 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 9 clinical features related to at least one miRs.

    • Correlation between mRNA expression and clinical features
      View Report | Testing the association between 17814 genes and 9 clinical features across 72 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 7 clinical features related to at least one genes.

    • Correlation between mRNAseq expression and clinical features
      View Report | Testing the association between 18278 genes and 12 clinical features across 533 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 9 clinical features related to at least one genes.

    • Correlation between mutation rate and clinical features
      View Report | Testing the association between 2 variables and 13 clinical features across 451 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 2 clinical features related to at least one variables.

    • Correlation between RPPA expression and clinical features
      View Report | Testing the association between 217 genes and 12 clinical features across 478 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 528 samples using the 29 copy number focal regions was identified for k = 6 clusters. We computed the clustering for k = 2 to k = 8 and used the cophenetic correlation coefficient to determine the best solution.

    • Clustering of copy number data by peak region with threshold value: consensus NMF
      View Report | The most robust consensus NMF clustering of 528 samples using the 29 copy number focal regions was identified for k = 6 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 most robust consensus NMF clustering of 319 samples using the 1842 most variable genes was identified for k = 4 clusters. We computed the clustering for k = 2 to k = 10 and uused the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

    • Clustering of miRseq mature expression: consensus hierarchical
      View Report | Median absolute deviation (MAD) was used to select 647 most variable miRs. Consensus ward linkage hierarchical clustering of 144 samples and 647 miRs identified 4 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

    • Clustering of miRseq mature expression: consensus NMF
      View Report | The most robust consensus NMF clustering of 144 samples using the 647 most variable miRs was identified for k = 4 clusters. We computed the clustering for k = 2 to k = 10 and uused the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

    • Clustering of miRseq precursor expression: consensus hierarchical
      View Report | Median absolute deviation (MAD) was used to select 115 most variable miRs. Consensus ward linkage hierarchical clustering of 516 samples and 115 miRs identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

    • Clustering of miRseq precursor expression: consensus NMF
      View Report | The most robust consensus NMF clustering of 516 samples using the 150 most variable miRs was identified for k = 5 clusters. We computed the clustering for k = 2 to k = 10 and uused the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

    • Clustering of mRNA expression: consensus hierarchical
      View Report | Median absolute deviation (MAD) was used to select 1500 most variable genes. Consensus ward linkage hierarchical clustering of 72 samples and 1500 genes identified 7 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

    • Clustering of mRNA expression: consensus NMF
      View Report | The most robust consensus NMF clustering of 72 samples using the 1500 most variable genes was identified for k = 3 clusters. We computed the clustering for k = 2 to k = 10 and uused the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

    • Clustering of mRNAseq gene expression: consensus hierarchical
      View Report | Median absolute deviation (MAD) was used to select 1500 most variable genes. Consensus ward linkage hierarchical clustering of 533 samples and 1500 genes identified 6 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

    • Clustering of mRNAseq gene expression: consensus NMF
      View Report | The most robust consensus NMF clustering of 533 samples using the 1500 most variable genes was identified for k = 5 clusters. We computed the clustering for k = 2 to k = 10 and uused the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

    • Clustering of RPPA data: consensus hierarchical
      View Report | Median absolute deviation (MAD) was used to select 217 most variable proteins. Consensus ward linkage hierarchical clustering of 478 samples and 217 proteins identified 4 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

    • Clustering of RPPA data: consensus NMF
      View Report | The most robust consensus NMF clustering of 478 samples using the 217 most variable proteins was identified for k = 6 clusters. We computed the clustering for k = 2 to k = 10 and uused the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

  • Other Analyses

    • Aggregate Analysis Features
      View Report | 538 samples and 1135 features are included in this feature table. The figures below show which genomic pair events are co-occurring and which are mutually-exclusive.

    • Identification of putative miR direct targets by sequencing data
      View Report | The CLR algorithm was applied on 685 miRs and 18278 mRNAs across 254 samples. After 2 filtering steps, the number of 148 miR:genes pairs were detected.

  • Pathway Analyses

    • Association of mutation, copy number alteration, and subtype markers with pathways
      View Report | There are 15 genes with significant mutation (Q value <= 0.1) and 394 genes with significant copy number alteration (Q value <= 0.25). The identified marker genes (Q value <= 0.01 or within top 2000) are 852 for subtype 1, 852 for subtype 2, 852 for subtype 3, 852 for subtype 4, 852 for subtype 5, 852 for subtype 6. Pathways significantly enriched with these genes (Q value <= 0.01) are identified :

    • GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in KIRC-TP
      View Report | basic data info

    • PARADIGM pathway analysis of mRNA expression and copy number data
      View Report | There were 61 significant pathways identified in this analysis.

    • PARADIGM pathway analysis of mRNA expression data
      View Report | There were 70 significant pathways identified in this analysis.

    • PARADIGM pathway analysis of mRNASeq expression and copy number data
      View Report | There were 40 significant pathways identified in this analysis.

    • PARADIGM pathway analysis of mRNASeq expression data
      View Report | There were 47 significant pathways identified in this analysis.

    • Significant over-representation of pathway gene sets for a given gene list
      View Report | For a given gene list, a hypergeometric test was tried to find significant overlapping canonical pathways using 1320 gene sets. In terms of FDR adjusted p.values, top 5 significant overlapping gene sets are listed as below.

  • Other Correlation Analyses

    • Correlation between copy number variation genes (focal events) and molecular subtypes
      View Report | Testing the association between copy number variation 29 focal events and 12 molecular subtypes across 528 patients, 205 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 12 molecular subtypes across 528 patients, 443 significant findings detected with P value < 0.05 and Q value < 0.25.

    • Correlation between gene mutation status and molecular subtypes
      View Report | Testing the association between mutation status of 25 genes and 12 molecular subtypes across 436 patients, 32 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 = 318. Number of gene expression samples = 533. Number of methylation samples = 319.

    • Correlations between copy number and mRNA expression
      View Report | The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are -0.1886, -0.06842, 0.0127, 0.0838, 0.1486, 0.2159, 0.2886, 0.3773, 0.48966, respectively.

    • Correlations between copy number and mRNAseq expression
      View Report | The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are 779.3, 1499, 1933, 2356, 2782, 3248.8, 3756, 4310, 5005.7, respectively.

Methods & Data
Input

  • Summary Report Date = Thu Apr 7 17:15:36 2016

  • Protection = FALSE

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