ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

By Guoliang Li, Melissa Jane Fullwood, Han Xu, F. Mulawadi, S. Velkov, V. Vega, P. Ariyaratne, Yusoff Bin Mohamed, H. Ooi, Chandana Tennakoon and 3 more. Genome Biology, 2010

325 citations recorded by the source corpus.

Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) is a new technology to study genome-wide long-range chromatin interactions bound by protein factors. Here we present ChIA-PET Tool, a software package for automatic processing of ChIA-PET sequence data, including linker filtering, mapping tags to reference genomes, identifying protein binding sites and chromatin interactions, and displaying the results on a graphical genome browser. ChIA-PET Tool is fast, accurate, comprehensive, user-friendly, and open source (available at http://chiapet.gis.a-star.edu.sg).

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d03e638a2cf88ac77dc4e441f2b8a218cad176c2

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Citations in the corpus

A decade of 3C technologies: insights into nuclear organization. (2012, methodology): “For a more thorough statistical definition of 4C, HiC, or ChIA-PET interactions, we refer to Lieberman-Aiden et al. (2009), Li et al. (2010), Splinter et al. (2011), and Yaffe and Tanay (2011).”
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient (2017, unknown): “A progression of high-throughput methods based on chromatin conformation capture (3C) (Dekker 2002) has emerged, including 4C (Simonis et al. 2006), 5C (Dostie et al. 2006), Hi-C (Lieberman-Aiden et al. 2009), ChIA-PET (Li et al. 2010), Capture Hi-C (Hughes et al. 2014; Mifsud et al.2015), andHiChIP”
Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data (2019, methodology): “The DNA – DNA contacts are computed using our developed method CHIA-PET Tool [53], and the procedures for processing of ChIA-PET sequence data are briefly given as below.”
Activation of proto-oncogenes by disruption of chromosome neighborhoods (2015, methodology): “pipeline was adapted from a previous report (8) and was recently developed based on multiple previous studies (15, 32, 39).”
ENCODE whole-genome data in the UCSC Genome Browser: update 2012 (2011, methodology): “New types of data available provided by UCSC this year include chromatin interaction maps by 5C (10) and ChIA-PET (11), nucleosome positioning by Mnase-seq , deep-sequenced DNAseI hypersensitive sites, SNP data for cell lines assayed for copy number variation, and three additional assays of RNA-bind”
The case for cloud computing in genome informatics (2010, background): “But these are also rapidly growing in size and complexity because of the drop in sequencing costs and the growth of derivative technologies such as chromatin immuno-precipitation with sequencing (ChIP-seq [32]), DNA methylation sequencing [33] and chromatin interaction mapping [34].”
Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes (2014, methodology): “The two biological replicates showed a high degree of correlation (Pearson's r > 0.91, Figure S1C, S1D), so we pooled the replicate data and processed it using an established protocol (Li et al., 2010), with modifications described in Extended Experimental Procedures (Figure S1, Table S1A).”
Extensive Promoter-centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation (2012, methodology): “The ChIA-PET sequence reads were analyzed using ChIA-PET Tool (Li et al., 2010).”
CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. (2015, methodology): “Short-read ChIA-PET data was previously generated by us and deposited in ENCODE data repository (Table S5) and processed using the original ChIAPET Tool (Li et al., 2010).”
ENCODE Data in the UCSC Genome Browser: year 5 update (2012, background): “Long-range chromatin looping interactions can be detected using various techniques, including chromosome conformation capture (9) and chromatin interaction analysis with paired-end tag (10).”
CTCF-Mediated Functional Chromatin Interactome in Pluripotent Cells (2011, background): “PETs with two ends mapped to different chromosomes (interchromosomally interacting PETs) or to the same chromosomes but spanning more than 10 kb (intrachromosomally interacting PETs) are candidates to define long-range chromatin interaction loc”