Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3)
AbstractUnderstanding chromatin interactions is important because they create chromosome conformation and link the cis- and trans- regulatory elements to their target genes for transcriptional regulation. Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing is a genome-wide high-throughput technology that detects chromatin interactions associated with a specific protein of interest. We developed ChIA-PET Tool for ChIA-PET data analysis in 2010. Here, we present the updated version of ChIA-PET Tool (V3) as a computational package to process the next-generation sequence data generated from ChIA-PET experiments. It processes short-read and long-read ChIA-PET data with multithreading and generates statistics of results in an HTML file. In this paper, we provide a detailed demonstration of the design of ChIA-PET Tool V3 and how to install it and analyze RNA polymerase II (RNAPII) ChIA-PET data from human K562 cells with it. We compared our tool with existing tools, including ChiaSig, MICC, Mango and ChIA-PET2, by using the same public data set in the same computer. Most peaks detected by the ChIA-PET Tool V3 overlap with those of other tools. There is higher enrichment for significant chromatin interactions from ChIA-PET Tool V3 in aggregate peak analysis (APA) plots. The ChIA-PET Tool V3 is publicly available at GitHub. View Full-Text
Share & Cite This Article
Li, G.; Sun, T.; Chang, H.; Cai, L.; Hong, P.; Zhou, Q. Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3). Genes 2019, 10, 554.
Li G, Sun T, Chang H, Cai L, Hong P, Zhou Q. Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3). Genes. 2019; 10(7):554.Chicago/Turabian Style
Li, Guoliang; Sun, Tongkai; Chang, Huidan; Cai, Liuyang; Hong, Ping; Zhou, Qiangwei. 2019. "Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3)." Genes 10, no. 7: 554.
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.