Literature DB >> 30753588

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

Weichun Huang1, Mario Medvedovic2, Jingwen Zhang3, Liang Niu2.   

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.
© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Year:  2019        PMID： 30753588      PMCID： PMC6468250          DOI： 10.1093/nar/gkz062

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  22 in total

1.  A Bayesian mixture model for chromatin interaction data.

Authors:  Liang Niu; Shili Lin
Journal:  Stat Appl Genet Mol Biol       Date:  2015-02

2.  Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.

Authors:  Guoliang Li; Xiaoan Ruan; Raymond K Auerbach; Kuljeet Singh Sandhu; Meizhen Zheng; Ping Wang; Huay Mei Poh; Yufen Goh; Joanne Lim; Jingyao Zhang; Hui Shan Sim; Su Qin Peh; Fabianus Hendriyan Mulawadi; Chin Thing Ong; Yuriy L Orlov; Shuzhen Hong; Zhizhuo Zhang; Steve Landt; Debasish Raha; Ghia Euskirchen; Chia-Lin Wei; Weihong Ge; Huaien Wang; Carrie Davis; Katherine I Fisher-Aylor; Ali Mortazavi; Mark Gerstein; Thomas Gingeras; Barbara Wold; Yi Sun; Melissa J Fullwood; Edwin Cheung; Edison Liu; Wing-Kin Sung; Michael Snyder; Yijun Ruan
Journal:  Cell       Date:  2012-01-20       Impact factor: 41.582

3.  An oestrogen-receptor-alpha-bound human chromatin interactome.

Authors:  Melissa J Fullwood; Mei Hui Liu; You Fu Pan; Jun Liu; Han Xu; Yusoff Bin Mohamed; Yuriy L Orlov; Stoyan Velkov; Andrea Ho; Poh Huay Mei; Elaine G Y Chew; Phillips Yao Hui Huang; Willem-Jan Welboren; Yuyuan Han; Hong Sain Ooi; Pramila N Ariyaratne; Vinsensius B Vega; Yanquan Luo; Peck Yean Tan; Pei Ye Choy; K D Senali Abayratna Wansa; Bing Zhao; Kar Sian Lim; Shi Chi Leow; Jit Sin Yow; Roy Joseph; Haixia Li; Kartiki V Desai; Jane S Thomsen; Yew Kok Lee; R Krishna Murthy Karuturi; Thoreau Herve; Guillaume Bourque; Hendrik G Stunnenberg; Xiaoan Ruan; Valere Cacheux-Rataboul; Wing-Kin Sung; Edison T Liu; Chia-Lin Wei; Edwin Cheung; Yijun Ruan
Journal:  Nature       Date:  2009-11-05       Impact factor: 49.962

4.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Authors:  Ben Langmead; Cole Trapnell; Mihai Pop; Steven L Salzberg
Journal:  Genome Biol       Date:  2009-03-04       Impact factor: 13.583

5.  Software for computing and annotating genomic ranges.

Authors:  Michael Lawrence; Wolfgang Huber; Hervé Pagès; Patrick Aboyoun; Marc Carlson; Robert Gentleman; Martin T Morgan; Vincent J Carey
Journal:  PLoS Comput Biol       Date:  2013-08-08       Impact factor: 4.475

6.  JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.

Authors:  Aziz Khan; Oriol Fornes; Arnaud Stigliani; Marius Gheorghe; Jaime A Castro-Mondragon; Robin van der Lee; Adrien Bessy; Jeanne Chèneby; Shubhada R Kulkarni; Ge Tan; Damir Baranasic; David J Arenillas; Albin Sandelin; Klaas Vandepoele; Boris Lenhard; Benoît Ballester; Wyeth W Wasserman; François Parcy; Anthony Mathelier
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971

7.  Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for mapping chromatin interactions and understanding transcription regulation.

Authors:  Yufen Goh; Melissa J Fullwood; Huay Mei Poh; Su Qin Peh; Chin Thing Ong; Jingyao Zhang; Xiaoan Ruan; Yijun Ruan
Journal:  J Vis Exp       Date:  2012-04-30       Impact factor: 1.355

8.  Model-based analysis of ChIP-Seq (MACS).

Authors:  Yong Zhang; Tao Liu; Clifford A Meyer; Jérôme Eeckhoute; David S Johnson; Bradley E Bernstein; Chad Nusbaum; Richard M Myers; Myles Brown; Wei Li; X Shirley Liu
Journal:  Genome Biol       Date:  2008-09-17       Impact factor: 13.583

9.  Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells.

Authors:  A Rasim Barutcu; Bryan R Lajoie; Rachel P McCord; Coralee E Tye; Deli Hong; Terri L Messier; Gillian Browne; Andre J van Wijnen; Jane B Lian; Janet L Stein; Job Dekker; Anthony N Imbalzano; Gary S Stein
Journal:  Genome Biol       Date:  2015-09-28       Impact factor: 13.583

10.  ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis.

Authors:  Guipeng Li; Yang Chen; Michael P Snyder; Michael Q Zhang
Journal:  Nucleic Acids Res       Date:  2016-09-12       Impact factor: 16.971
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  3 in total

Review 1.  3D chromatin architecture and transcription regulation in cancer.

Authors:  Siwei Deng; Yuliang Feng; Siim Pauklin
Journal:  J Hematol Oncol       Date:  2022-05-04       Impact factor: 23.168

Review 2.  The Many Faces of Gene Regulation in Cancer: A Computational Oncogenomics Outlook.

Authors:  Enrique Hernández-Lemus; Helena Reyes-Gopar; Jesús Espinal-Enríquez; Soledad Ochoa
Journal:  Genes (Basel)       Date:  2019-10-30       Impact factor: 4.096

3.  Bacon: a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies.

Authors:  Li Tang; Matthew C Hill; Patrick T Ellinor; Min Li
Journal:  Genome Biol       Date:  2022-01-21       Impact factor: 13.583
  3 in total

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