Analysis Overview
Cervical Squamous Cell Carcinoma (Primary solid tumor)
21 April 2013 | analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C14F1NNJ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Analysis Overview for Cervical Squamous Cell Carcinoma (Primary solid tumor cohort) - 21 April 2013. Broad Institute of MIT and Harvard. doi:10.7908/C14F1NNJ
Overview
Introduction

This is an overview of Cervical Squamous Cell Carcinoma analysis pipelines from Firehose run "21 April 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 126 tumor samples used in this analysis: 23 significant arm-level results, 24 significant focal amplifications, and 28 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 126 samples using the 52 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 9110 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 134 samples and 9110 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 mRNAseq gene expression: consensus NMF
  View Report | The most robust consensus NMF clustering of 116 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 | The 1500 most variable genes were selected. Consensus average linkage hierarchical clustering of 116 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 134 samples and 150 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 | We filtered the data to 150 most variable miRs. Consensus average linkage hierarchical clustering of 134 samples and 150 miRs 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.

- Correlation Analyses

- Correlation between copy number variations of arm-level result and selected clinical features
  View Report | Testing the association between copy number variation 44 arm-level results and 10 clinical features across 34 patients, 2 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 51 arm-level results and 10 clinical features across 34 patients, no significant finding detected with Q value < 0.25.

- Correlation between gene methylation status and clinical features
  View Report | Testing the association between 17326 genes and 9 clinical features across 33 samples, statistically thresholded by Q value < 0.05, 2 clinical features related to at least one genes.

- Correlation between molecular cancer subtypes and selected clinical features
  View Report | Testing the association between subtypes identified by 6 different clustering approaches and 10 clinical features across 40 patients, no significant finding 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 7 genes and 9 clinical features across 21 patients, no significant finding detected with Q value < 0.25.

- Correlation between mRNAseq expression and clinical features
  View Report | Testing the association between 18258 genes and 9 clinical features across 36 samples, statistically thresholded by Q value < 0.05, 1 clinical feature related to at least one genes.

- Correlation between miRseq expression and clinical features
  View Report | Testing the association between 540 genes and 9 clinical features across 40 samples, statistically thresholded by Q value < 0.05, 1 clinical feature 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 1155.5, 1884, 2481, 3048, 3656.5, 4320, 5032.5, 5780, 6624.5, respectively.

- Correlation between mRNA expression and DNA methylation
  View Report | The top 25 correlated methylation probes per gene are displayed. Total number of matched samples = 116. Number of gene expression samples = 116. Number of methylation samples = 116.

- Correlation between copy number variations of arm-level result and molecular subtypes
  View Report | Testing the association between copy number variation 73 arm-level results and 6 molecular subtypes across 126 patients, 6 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 52 peak regions and 6 molecular subtypes across 126 patients, 12 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 9 genes and 6 molecular subtypes across 39 patients, no significant finding 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 23 significant subnetworks identified in HotNet analysis.

- PARADIGM pathway analysis of mRNASeq expression data
  View Report | There were 48 significant pathways identified in this analysis.

- PARADIGM pathway analysis of mRNASeq expression and copy number data
  View Report | There were 42 significant pathways identified in this analysis.

Methods & Data
Input

- Summary Report Date = Sat May 25 13:14:35 2013

- Protection = FALSE

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