Bioinformatics and data integration

Coordinator:		Dr. Ralf Herwig
Institution:		Max Planck Institut für molekulare Genetik
Homepage:		www.molgen.mpg.de

The overall research goal of the IG is the systematic identification of key modifier genes acting through genomic (promoter) methylation and their corresponding target sets in the context of colon cancer tumor progression and carcinogenesis. Data will be generated with colon cancer patients and mouse chromosome substitution strains (CSSs). These biological systems will be analysed with next generation sequencing on the transcriptome and methylome level (MeDIP) using an iteration of refined genetic engineering of mouse models, genotyping, methylome analysis in order to identify cancer modifiers and their target genes.
Main goal of the subproject 6 (“Bioinformatics and data integration”) is to build the computational framework for the IG, in particular an integrated framework for data analysis, data correlation, genetic analysis and pathway analysis.
In the course of this IG we plan
1.) to apply an existing XML-based data integration system and to embed the project data in existing standards and to develop new standards for next generation sequencing data,
2.) to set up a pipeline for analysis of transcriptome and methylation screens (MeDIP) based on next generation sequencing data (for example Illumina/Solexa) in mouse and colon cancer patients,
3.) to identify modifier genes and targets through genetic analysis of CSSs,
4.) to extend our current pathway integration system (ConsensusPathDB) with methylation events, to relate these events with molecular reaction networks and to annotate a modifier network relevant for epigenetic control of colon cancer tumor formation and progression,
5.) to develop a prototype for the efficient management, analysis and functional interpretation of next generation sequencing data.