Analysis Overview
Rectum Adenocarcinoma (Primary solid tumor)
17 October 2014 | analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1S46QW6
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Analysis Overview for Rectum Adenocarcinoma (Primary solid tumor cohort) - 17 October 2014. Broad Institute of MIT and Harvard. doi:10.7908/C1S46QW6
Overview
Introduction

This is an overview of Rectum Adenocarcinoma analysis pipelines from Firehose run "17 October 2014".

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 1.0.5 (Cancer-Specific High-throughput Annotation of Somatic Mutations)
  View Report | There are 84 mutations identified by MuTect and 11 mutations with significant functional impact at BHFDR <= 0.25.

- LowPass Copy number analysis (GISTIC2)
  View Report | There were 35 tumor samples used in this analysis: 18 significant arm-level results, 7 significant focal amplifications, and 3 significant focal deletions were found.

- Mutation Analysis (MutSig 2CV v3.1)
  View Report |

- Mutation Analysis (MutSig v1.5)
  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 165 tumor samples used in this analysis: 20 significant arm-level results, 24 significant focal amplifications, and 35 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 169 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 59 focal events and 12 clinical features across 165 patients, no significant finding 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 78 arm-level events and 12 clinical features across 165 patients, no significant finding detected with Q value < 0.25.

- Correlation between gene methylation status and clinical features
  View Report | Testing the association between 20103 genes and 12 clinical features across 98 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 1 clinical feature related to at least one genes.

- Correlation between gene mutation status and selected clinical features
  View Report | Testing the association between mutation status of 12 genes and 10 clinical features across 69 patients, no significant finding detected with Q value < 0.25.

- Correlation between miRseq expression and clinical features
  View Report | Testing the association between 427 miRs and 12 clinical features across 143 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 4 clinical features related to at least one miRs.

- Correlation between mRNA expression and clinical features
  View Report | Testing the association between 17814 genes and 10 clinical features across 69 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 2 clinical features related to at least one genes.

- Correlation between mRNAseq expression and clinical features
  View Report | Testing the association between 18107 genes and 12 clinical features across 163 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 7 clinical features related to at least one genes.

- Correlation between mutation rate and clinical features
  View Report | Testing the association between 2 variables and 11 clinical features across 69 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 171 genes and 12 clinical features across 130 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 6 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 165 samples using the 59 copy number focal regions 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 copy number data by peak region with threshold value: consensus NMF
  View Report | The most robust consensus NMF clustering of 165 samples using the 59 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 6787 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 98 samples and 6787 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 | Median absolute deviation (MAD) was used to select 647 most variable miRs. Consensus ward linkage hierarchical clustering of 51 samples and 647 miRs identified 5 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

- Clustering of miRseq mature expression: consensus NMF
  View Report | We filtered the data to 647 most variable miRs. Consensus NMF clustering of 51 samples and 647 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 hierarchical
  View Report | Median absolute deviation (MAD) was used to select 106 most variable miRs. Consensus ward linkage hierarchical clustering of 143 samples and 106 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 | We filtered the data to 150 most variable miRs. Consensus NMF clustering of 143 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 mRNA expression: consensus hierarchical
  View Report | Median absolute deviation (MAD) was used to select 1500 most variable genes. Consensus ward linkage hierarchical clustering of 69 samples and 1500 genes identified 8 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 69 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 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 163 samples and 1500 genes identified 4 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 163 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 | Median absolute deviation (MAD) was used to select 171 most variable proteins. Consensus ward linkage hierarchical clustering of 130 samples and 171 proteins identified 6 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 130 samples using 171 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

- Aggregate Analysis Features
  View Report | 171 samples and 393 features are included in this feature table. The figures below show which genomic pair events are co-occurring and which are mutually-exclusive.

- Pathway Analyses

- Association of mutation, copy number alteration, and subtype markers with pathways
  View Report | There are 11 genes with significant mutation (Q value <= 0.1) and 443 genes with significant copy number alteration (Q value <= 0.25). The identified marker genes (Q value <= 0.01 or within top 2000) are 2000 for subtype 1, 2000 for subtype 2, 2000 for subtype 3, 2000 for subtype 4. Pathways significantly enriched with these genes (Q value <= 0.01) are identified :

- PARADIGM pathway analysis of mRNA expression and copy number data
  View Report | There were 22 significant pathways identified in this analysis.

- PARADIGM pathway analysis of mRNA expression data
  View Report | There were 31 significant pathways identified in this analysis.

- PARADIGM pathway analysis of mRNASeq expression and copy number data
  View Report | There were 28 significant pathways identified in this analysis.

- PARADIGM pathway analysis of mRNASeq expression data
  View Report | There were 23 significant pathways identified in this analysis.

- Other Correlation Analyses

- Correlation between copy number variation genes (focal events) and molecular subtypes
  View Report | Testing the association between copy number variation 59 focal events and 12 molecular subtypes across 165 patients, 12 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 78 arm-level events and 12 molecular subtypes across 165 patients, 8 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 12 genes and 9 molecular subtypes across 69 patients, 2 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 = 95. Number of gene expression samples = 163. Number of methylation samples = 98.

- Correlations between copy number and mRNA expression
  View Report | The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are -0.07236, 0.0082, 0.07502, 0.1425, 0.2071, 0.27744, 0.346, 0.4246, 0.51846, 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 842, 1642, 2216.8, 2789.4, 3379, 3935, 4497, 5095, 5808, respectively.

Methods & Data
Input

- Summary Report Date = Wed Jan 21 17:32:44 2015

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