Comprehensive analysis of these heterogeneous data requires a collaborative effort of a team of bioinformaticians and infrastructure that facilitates the integration of several analysis and data sources. We have analyzed temozolomide treated glioblastoma patient data using the Anduril analysis framework. Our analysis demonstrates the importance of involving multiple data sources and analysis methods in a structured and comprehensive analysis of large-scale cancer data. The analysis is implemented as a workflow in the Anduril bioinformatics framework.

Results

Analysis results for GBM patients submitted to the CAMDA'11 challenge.

• Abstract
• Result website for temozolomide treated patient subgroup.
• Result website for the complete set of glioblastoma patients available from the Cancer Genome Atlas.
• Configuration report for the temozolomide subgroup analysis.
• Enzyme substitutions in GBM (analysis report).
• EGFRvIII analysis including exonic expression and survival results.
• MiRNA targets from the enzyme substitution pairs.

Source codes

All the source codes are available unrestricted. The analysis has been written in AnduriScript using Anduril components. The Anduril component API gives additional details for the components. Below you will find descriptions and direct links to some of the more central parts of the analysis.

• Main analysis
• Read-in function for fetching TCGA data and the GetFromTCGA component description.
• Array CGH analysis
• Array CGH analysis function collection 2
• Gene expression analysis based on median exon expression
• Methylation status analysis
• Genotype specific survival analysis
• Summary website generator
• Enzyme substitution analysis
• EGFRvIII mutant analysis

Related websites

• Anduril bioinformatics framework
• Moksiskaan pathway integration tool for Anduril
• pint R package and Anduril component for the dependency analysis

Anduril citation

• Kristian Ovaska, Marko Laakso et al. Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme. Genome Medicine 2010, 2:65.