Analysis Overview for Stomach Adenocarcinoma
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

This is the analysis overview for Firehose run "26 March 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 306 tumor samples used in this analysis: 26 significant arm-level results, 29 significant focal amplifications, and 46 significant focal deletions were found.

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

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

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

- 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 306 samples using the 75 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 6210 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 260 samples and 6210 genes 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 mRNAseq gene expression: consensus NMF
  View Report | The most robust consensus NMF clustering of 43 samples using the 1500 most variable genes was identified for k = 2 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 | The 1500 most variable genes were selected. Consensus average linkage hierarchical clustering of 43 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 miRseq precursor expression: consensus NMF
  View Report | We filtered the data to 150 most variable miRs. Consensus NMF clustering of 237 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 hierarchical
  View Report | We filtered the data to 150 most variable miRs. Consensus average linkage hierarchical clustering of 237 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.

- Correlation Analyses

- Correlation between copy number variations of arm-level result and selected clinical features
  View Report | Testing the association between copy number variation 74 arm-level results and 11 clinical features across 177 patients, 5 significant findings detected with Q value < 0.25.

- Correlation between copy number variation genes (focal) and selected clinical features
  View Report | Testing the association between copy number variation 75 arm-level results and 11 clinical features across 177 patients, one significant finding detected with Q value < 0.25.

- Correlation between molecular cancer subtypes and selected clinical features
  View Report | Testing the association between subtypes identified by 6 different clustering approaches and 11 clinical features across 178 patients, 4 significant findings detected with P value < 0.05 and Q value < 0.25.

- Correlation between gene mutation status and selected clinical features
  View Report | Testing the association between mutation status of 47 genes and 10 clinical features across 116 patients, 6 significant findings detected with Q value < 0.25.

- Correlation between mRNAseq expression and clinical features
  View Report | Testing the association between 19433 genes and 10 clinical features across 43 samples, statistically thresholded by Q value < 0.05, 6 clinical features related to at least one genes.

- Correlation between miRseq expression and clinical features
  View Report | Testing the association between 533 genes and 11 clinical features across 165 samples, statistically thresholded by Q value < 0.05, 5 clinical features related to at least one genes.

- Correlations between copy number and mRNAseq expression
  View Report | The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are 1119.2, 2319.4, 3065.6, 3788, 4531, 5252, 6000.4, 6791, 7666.8, respectively.

- Correlation between copy number variations of arm-level result and molecular subtypes
  View Report | Testing the association between copy number variation 77 arm-level results and 6 molecular subtypes across 306 patients, 62 significant findings detected with Q value < 0.25.

- Correlation between copy number variation genes and molecular subtypes
  View Report | Testing the association between copy number variation of 75 peak regions and 6 molecular subtypes across 306 patients, 133 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 47 genes and 6 molecular subtypes across 116 patients, 7 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 | There were 47 significant subnetworks identified in HotNet analysis.

- PARADIGM pathway analysis of mRNASeq expression data
  View Report | There were 18 significant pathways identified in this analysis.

- PARADIGM pathway analysis of mRNASeq expression and copy number data
  View Report | There were 11 significant pathways identified in this analysis.

Methods & Data
Input

- Run Prefix = analyses__2013_03_26

- Summary Report Date = Sat Apr 20 08:47:09 2013

- Protection = FALSE

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