Chromatin immunoprecipitation combined with sequencing (ChIP-seq) is a biological method to analyse the interactions of DNA and certain proteins. From a bioinformatician's point of view, the challenge of the analysis lies in identifying a potentially very weak signal among a level of noise. A multitude of algorithms, different normalization methods and further downstream analyses are available, but choosing the best options for a particular data set is usually no trivial task.
In cooperation with the Institute of Molecular Tumor Biology of the University of Münster, we have analysed a number of ChIP-seq data sets. The combination of ChIP-seq analysis and complementary gene expression data is here of special interest.