MACPET: model-based analysis for ChIA-PET

Ioannis Vardaxis; Finn Drabløs; Morten B Rye; Bo Henry Lindqvist

doi:10.1093/biostatistics/kxy084

MACPET: model-based analysis for ChIA-PET

Biostatistics. 2020 Jul 1;21(3):625-639. doi: 10.1093/biostatistics/kxy084.

Authors

Ioannis Vardaxis¹, Finn Drabløs², Morten B Rye³, Bo Henry Lindqvist¹

Affiliations

¹ Department of Mathematical Sciences, Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
² Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
³ Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, N-7491 Trondheim, Norway and Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, N-7030 Trondheim, Norway.

Abstract

We 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.

Keywords: ChIA-PET; MACPET; Model-based clustering; Paired-end tags; Peak-calling algorithm.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chromatin Immunoprecipitation Sequencing*
Chromatin Immunoprecipitation*
Genome*
High-Throughput Nucleotide Sequencing*
Humans
Models, Biological*
Protein Binding*
Sequence Analysis, DNA*