Biomaterial Database

ChIAPoP: a new tool for ChIA-PET data analysis. 2019

Weichun Huang, and Mario Medvedovic, and Jingwen Zhang, and Liang Niu

National Exposure Research Laboratory, Environmental Protection Agency, Research Triangle Park, NC 27709, USA.

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.

UI	MeSH Term	Description	Entries
D002843	Chromatin	The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.	Chromatins
D006801	Humans	Members of the species Homo sapiens.	Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000076246	CCCTC-Binding Factor	A repressor protein with poly(ADP)-ribose binding activity that binds CHROMATIN and DNA; its structure consisting of 11 CYS2-HIS2 ZINC FINGERS allows it to recognize many different DNA target sites. It functions as a repressor by binding to INSULATOR ELEMENTS and preventing interaction between promoters and nearby enhancers and silencers. It plays a critical role in EPIGENETIC PROCESSES, including GENOMIC IMPRINTING.	CTCF Protein,DNA-Binding Protein CTCF,CCCTC Binding Factor,CTCF, DNA-Binding Protein,DNA Binding Protein CTCF
D000078332	Data Analysis	Process of systematically applying statistical and/or logical techniques to describe and illustrate, condense and recap, and evaluate data (https://ori.hhs.gov/education).	Analyses, Data,Analysis, Data,Data Analyses
D001483	Base Sequence	The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.	DNA Sequence,Nucleotide Sequence,RNA Sequence,DNA Sequences,Base Sequences,Nucleotide Sequences,RNA Sequences,Sequence, Base,Sequence, DNA,Sequence, Nucleotide,Sequence, RNA,Sequences, Base,Sequences, DNA,Sequences, Nucleotide,Sequences, RNA
D001665	Binding Sites	The parts of a macromolecule that directly participate in its specific combination with another molecule.	Combining Site,Binding Site,Combining Sites,Site, Binding,Site, Combining,Sites, Binding,Sites, Combining
D016012	Poisson Distribution	A distribution function used to describe the occurrence of rare events or to describe the sampling distribution of isolated counts in a continuum of time or space.	Distribution, Poisson
D017422	Sequence Analysis, DNA	A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.	DNA Sequence Analysis,Sequence Determination, DNA,Analysis, DNA Sequence,DNA Sequence Determination,DNA Sequence Determinations,DNA Sequencing,Determination, DNA Sequence,Determinations, DNA Sequence,Sequence Determinations, DNA,Analyses, DNA Sequence,DNA Sequence Analyses,Sequence Analyses, DNA,Sequencing, DNA
D045744	Cell Line, Tumor	A cell line derived from cultured tumor cells.	Tumor Cell Line,Cell Lines, Tumor,Line, Tumor Cell,Lines, Tumor Cell,Tumor Cell Lines