MACPET: model-based analysis for ChIA-PET

• DOI: 10.1093/biostatistics/kxy084
• Publication Date: 2018-12-19T20:12:37Z
• Authors: Ioannis Vardaxis; Finn Drabløs; Morten B Rye; Bo Henry Lindqvist
• Keywords: Chromatin Immunoprecipitation; Genome; 0206 medical engineering; Chromatin Immunoprecipitation Sequencing; High-Throughput Nucleotide Sequencing; Humans; Articles; Sequence Analysis, DNA; 02 engineering and technology; Models, Biological; Protein Binding

SummaryWe present model-based analysis for ChIA-PET (MACPET), which analyzes paired-end read sequences provided by ChIA-PET for finding binding sites of a protein of interest. MACPET uses information from both tags of each PET and searches for binding sites in a two-dimensional space, while taking into account different noise levels in different genomic regions. MACPET shows favorable results compared with MACS in terms of motif occurrence and spatial resolution. Furthermore, significant binding sites discovered by MACPET are involved in a higher number of significant three-dimensional interactions than those discovered by MACS. MACPET is freely available on Bioconductor. ChIA-PET; MACPET; Model-based clustering; Paired-end tags; Peak-calling algorithm.