Analysis Overview for Cervical Squamous Cell Carcinoma
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
Overview
Introduction

This is the analysis overview for Firehose run "25 July 2012".

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 68 tumor samples used in this analysis: 21 significant arm-level results, 16 significant focal amplifications, and 19 significant focal deletions were found.

- Mutation Analysis (MutSig)
  View Report | Significantly mutated genes (q ≤ 0.1): 4

- Clustering Analyses

- Clustering of miRseq expression: consensus NMF
  View Report | We filtered the data to 150 most variable miRs. Consensus NMF clustering of 42 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 42 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.

- Correlation Analyses

- Correlation between molecular cancer subtypes and selected clinical features
  View Report | Testing the association between subtypes identified by 2 different clustering approaches and 4 clinical features across 17 patients, no significant finding detected with P value < 0.05.

- Correlation between gene mutation status and selected clinical features
  View Report | Testing the association between 'NFE2L2 MUTATION ANALYSIS' and 2 clinical features across 12 patients, no significant finding detected with Q value < 0.25.

- Other Analyses

- Correlation between copy number variations of arm-level result and selected clinical features
  View Report | Testing the association between copy number variation 20 arm-level results and 2 clinical features across 14 patients, no significant finding detected with Q value < 0.25.

- Correlation between copy number variation genes and selected clinical features
  View Report | Testing the association between copy number variation of 18 peak regions and 2 clinical features across 14 patients, no significant finding detected with Q value < 0.25.

Methods & Data
Input

- Run Prefix = analyses__2012_07_25

- Summary Report Date = Fri Aug 17 15:02:50 2012

- Protection = FALSE

Copyright © 2011 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle