This is the analysis overview for Firehose run "25 May 2012".
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.
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Sequence and Copy Number Analyses
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Copy number analysis (GISTIC2)
View Report | There were 132 tumor samples used in this analysis: 17 significant arm-level results, 23 significant focal amplifications, and 36 significant focal deletions were found. -
Mutation Analysis (MutSig)
View Report | Significantly mutated genes (q ≤ 0.1): 141 -
Clustering Analyses
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Clustering of mRNAseq gene expression: consensus NMF
View Report | The most robust consensus NMF clustering of 57 samples using the 1500 most variable genes was identified for k = 5 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 57 samples and 1500 genes identified 2 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 Methylation: consensus NMF
View Report | The 859 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 64 samples and 859 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 expression: consensus NMF
View Report | We filtered the data to 150 most variable miRs. Consensus NMF clustering of 123 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 expression: consensus hierarchical
View Report | We filtered the data to 150 most variable miRs. Consensus average linkage hierarchical clustering of 123 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. -
Other Analyses
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Correlation between molecular cancer subtypes and selected clinical features
View Report | Testing the association between subtypes identified by 5 different clustering approaches and 8 clinical features across 124 patients, 4 significant findings detected with P value < 0.05. -
Correlation between gene mutation status and selected clinical features
View Report | Testing the association between mutation status of 245 genes and 8 clinical features across 132 patients, 3 significant findings detected with Q value < 0.25. -
Correlations between copy number and mRNAseq expression
View Report | The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are 1060.2, 2147, 2850.6, 3529.8, 4215, 4900, 5561, 6313, 7139.8, respectively.
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Firehose Directory = /local/cga-fh/tcga-gdac
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Run Prefix = analyses__2012_05_25
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Summary Report Date = Sat Jun 16 13:20:44 2012
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Protection = FALSE