Literature DB >> 23872977

Statistical analysis of ChIP-seq data with MOSAiCS.

Guannan Sun1, Dongjun Chung, Kun Liang, Sündüz Keleş.   

Abstract

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is invaluable for identifying genome-wide binding of transcription factors and mapping of epigenomic profiles. We present a statistical protocol for analyzing ChIP-seq data. We describe guidelines for data preprocessing and quality control and provide detailed examples of identifying ChIP-enriched regions using the Bioconductor package "mosaics."

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Substances:

Year:  2013        PMID: 23872977     DOI: 10.1007/978-1-62703-514-9_12

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  12 in total

1.  Histone H3.3 G34 mutations promote aberrant PRC2 activity and drive tumor progression.

Authors:  Siddhant U Jain; Sima Khazaei; Dylan M Marchione; Stefan M Lundgren; Xiaoshi Wang; Daniel N Weinberg; Shriya Deshmukh; Nikoleta Juretic; Chao Lu; C David Allis; Benjamin A Garcia; Nada Jabado; Peter W Lewis
Journal:  Proc Natl Acad Sci U S A       Date:  2020-10-16       Impact factor: 11.205

Review 2.  Genomics pipelines and data integration: challenges and opportunities in the research setting.

Authors:  Jeremy Davis-Turak; Sean M Courtney; E Starr Hazard; W Bailey Glen; Willian A da Silveira; Timothy Wesselman; Larry P Harbin; Bethany J Wolf; Dongjun Chung; Gary Hardiman
Journal:  Expert Rev Mol Diagn       Date:  2017-01-25       Impact factor: 5.225

3.  Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape.

Authors:  Chao Lu; Siddhant U Jain; Dominik Hoelper; Denise Bechet; Rosalynn C Molden; Leili Ran; Devan Murphy; Sriram Venneti; Meera Hameed; Bruce R Pawel; Jay S Wunder; Brendan C Dickson; Stefan M Lundgren; Krupa S Jani; Nicolas De Jay; Simon Papillon-Cavanagh; Irene L Andrulis; Sarah L Sawyer; David Grynspan; Robert E Turcotte; Javad Nadaf; Somayyeh Fahiminiyah; Tom W Muir; Jacek Majewski; Craig B Thompson; Ping Chi; Benjamin A Garcia; C David Allis; Nada Jabado; Peter W Lewis
Journal:  Science       Date:  2016-05-13       Impact factor: 47.728

4.  Reassessment of Piwi binding to the genome and Piwi impact on RNA polymerase II distribution.

Authors:  Haifan Lin; Mengjie Chen; Anshul Kundaje; Anton Valouev; Hang Yin; Na Liu; Nils Neuenkirchen; Mei Zhong; Michael Snyder
Journal:  Dev Cell       Date:  2015-03-23       Impact factor: 12.270

5.  Dynamic regulation of Schwann cell enhancers after peripheral nerve injury.

Authors:  Holly A Hung; Guannan Sun; Sunduz Keles; John Svaren
Journal:  J Biol Chem       Date:  2015-01-22       Impact factor: 5.157

6.  The essential Rhodobacter sphaeroides CenKR two-component system regulates cell division and envelope biosynthesis.

Authors:  Bryan D Lakey; Kevin S Myers; François Alberge; Erin L Mettert; Patricia J Kiley; Daniel R Noguera; Timothy J Donohue
Journal:  PLoS Genet       Date:  2022-06-29       Impact factor: 6.020

7.  Ritornello: high fidelity control-free chromatin immunoprecipitation peak calling.

Authors:  Kelly P Stanton; Jiaqi Jin; Roy R Lederman; Sherman M Weissman; Yuval Kluger
Journal:  Nucleic Acids Res       Date:  2017-12-01       Impact factor: 16.971

Review 8.  Identifying and mitigating bias in next-generation sequencing methods for chromatin biology.

Authors:  Clifford A Meyer; X Shirley Liu
Journal:  Nat Rev Genet       Date:  2014-09-16       Impact factor: 53.242

9.  Fungal Morphology, Iron Homeostasis, and Lipid Metabolism Regulated by a GATA Transcription Factor in Blastomyces dermatitidis.

Authors:  Amber J Marty; Aimee T Broman; Robert Zarnowski; Teigan G Dwyer; Laura M Bond; Anissa Lounes-Hadj Sahraoui; Joël Fontaine; James M Ntambi; Sündüz Keleş; Christina Kendziorski; Gregory M Gauthier
Journal:  PLoS Pathog       Date:  2015-06-26       Impact factor: 6.823

10.  Identifying TF-MiRNA Regulatory Relationships Using Multiple Features.

Authors:  Mingyu Shao; Yanni Sun; Shuigeng Zhou
Journal:  PLoS One       Date:  2015-04-29       Impact factor: 3.240

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