ChIAPoP: a new tool for ChIA-PET data analysis

Nucleic Acids Res. 2019 Apr 23;47(7):e37. doi: 10.1093/nar/gkz062.

Abstract

Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) is a popular assay method for studying genome-wide chromatin interactions mediated by a protein of interest. The main goal of ChIA-PET data analysis is to detect interactions between DNA regions. Here, we propose a new method and the associated data analysis pipeline, ChIAPoP, to detect chromatin interactions from ChIA-PET data. We compared ChIAPoP with other popular methods, including a hypergeometric model (used in ChIA-PET tool), MICC (used in ChIA-PET2), ChiaSig and mango. The results showed that ChIA-PoP performed better than or at least as well as these top existing methods in detecting true chromatin interactions. ChIAPoP is freely available to the public at https://github.com/wh90999/ChIAPoP.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Sequence
  • Binding Sites / genetics
  • CCCTC-Binding Factor / metabolism
  • Cell Line, Tumor
  • Chromatin / metabolism*
  • Data Analysis
  • Humans
  • Poisson Distribution
  • Sequence Analysis, DNA

Substances

  • CCCTC-Binding Factor
  • CTCF protein, human
  • Chromatin