An integrated ChIP-seq analysis platform with customizable workflows

BMC Bioinformatics
Eugenia Giannopoulou, Olivier Elemento

Abstract

Chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq), enables unbiased and genome-wide mapping of protein-DNA interactions and epigenetic marks. The first step in ChIP-seq data analysis involves the identification of peaks (i.e., genomic locations with high density of mapped sequence reads). The next step consists of interpreting the biological meaning of the peaks through their association with known genes, pathways, regulatory elements, and integration with other experiments. Although several programs have been published for the analysis of ChIP-seq data, they often focus on the peak detection step and are usually not well suited for thorough, integrative analysis of the detected peaks. To address the peak interpretation challenge, we have developed ChIPseeqer, an integrative, comprehensive, fast and user-friendly computational framework for in-depth analysis of ChIP-seq datasets. The novelty of our approach is the capability to combine several computational tools in order to create easily customized workflows that can be adapted to the user's needs and objectives. In this paper, we describe the main components of the ChIPseeqer framework, and also demonstrate the utility and diversity of the analys...Continue Reading

References

Oct 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·A SethT S Papas
Aug 3, 2000·The New England Journal of Medicine·S ViskinB Belhassen
Mar 29, 2001·Nature Immunology·S FeskeA Rao
Dec 26, 2001·Nucleic Acids Research·Minoru KanehisaAkihiro Nakaya
Feb 16, 2002·Science·Job DekkerNancy Kleckner
Dec 19, 2003·Nucleic Acids Research·Albin SandelinBoris Lenhard
Feb 12, 2004·Bioinformatics·M J L de HoonS Miyano
Jun 8, 2004·Bioinformatics·Alok J Saldanha
Jun 24, 2004·International Immunology·Myeong Sup LeeJoseph M McCune
Oct 23, 2004·Nucleic Acids Research·Peter C HollenhorstBarbara J Graves
Oct 23, 2004·Science·ENCODE Project Consortium
Jul 19, 2005·Genome Research·Adam SiepelDavid Haussler
Sep 20, 2005·Genome Research·Belinda GiardineAnton Nekrutenko
May 4, 2006·Human Mutation·Jared M BischofTerry A Braun
Jul 18, 2006·Nucleic Acids Research·Xuwo JiX Shirley Liu
Jun 2, 2007·Science·David S JohnsonBarbara Wold
Jul 3, 2007·Nature·Tarjei S MikkelsenBradley E Bernstein
Oct 30, 2007·Molecular Cell·Olivier ElementoSaeed Tavazoie
Nov 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Ting WangDavid Haussler
Apr 23, 2008·Current Protocols in Bioinformatics·James TaylorAnton Nekrutenko
Jun 3, 2008·Nature Methods·Ali MortazaviBarbara Wold
Jul 17, 2008·Comparative and Functional Genomics·Jennifer Williams, William Andersen
Aug 5, 2008·Biochimica Et Biophysica Acta·Stephan Kadauke, Gerd A Blobel
Aug 8, 2008·Nucleic Acids Research·Raja JothiKeji Zhao
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Oct 10, 2008·Nucleic Acids Research·Daniel E Newburger, Martha L Bulyk
Nov 4, 2008·Nature Biotechnology·Hongkai JiWing H Wong
Dec 17, 2008·BMC Bioinformatics·Arnaud R KrebsLaszlo Tora
Jan 6, 2009·Nature Biotechnology·Joel RozowskyMark B Gerstein
Jan 23, 2009·Nature Methods·Anton ValouevArend Sidow
Feb 13, 2009·Nature·Axel ViselLen A Pennacchio
Mar 12, 2009·Methods : a Companion to Methods in Enzymology·Dominic SchmidtDuncan T Odom
Jun 10, 2009·Bioinformatics·Heng Li1000 Genome Project Data Processing Subgroup
Aug 20, 2009·Bioinformatics·Hyunjin ShinX Shirley Liu
Sep 9, 2009·Nature Reviews. Genetics·Peter J Park
Sep 24, 2009·BMC Bioinformatics·Christiana SpyrouSimon Tavaré
Nov 3, 2009·Nature Methods·Shirley PepkeAli Mortazavi
Nov 19, 2009·Nucleic Acids Research·Kate R RosenbloomW James Kent
Dec 17, 2009·Molecular Cell·Hani GoodarziSaeed Tavazoie
Dec 19, 2009·PLoS Genetics·Peter C HollenhorstBarbara J Graves
Jan 14, 2010·Current Protocols in Molecular Biology·Daniel BlankenbergJames Taylor
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
May 4, 2010·Nature Biotechnology·Cory Y McLeanGill Bejerano
Jun 22, 2010·Bioinformatics·Daniel BlankenbergGalaxy Team
Jul 6, 2010·BMC Bioinformatics·Zhaohui S QinArul M Chinnaiyan
Aug 10, 2010·BMC Bioinformatics·Mali Salmon-DivonPaul Bertone
Nov 4, 2010·Nucleic Acids Research·Darby Tien-Hao ChangWei-Sheng Wu
Nov 18, 2010·Methods in Molecular Biology·Peter D'Eustachio
Nov 26, 2010·Genes & Development·Grant D BarishRonald M Evans
Dec 7, 2010·Nucleic Acids Research·Daniel HebenstreitSarah A Teichmann
Dec 24, 2010·Nucleic Acids Research·Tao YeLaszlo Tora
Jan 14, 2011·BMC Bioinformatics·Valerie HowerLior Pachter
Feb 2, 2011·BMC Bioinformatics·Peter HumburgGlenn Stone
Mar 10, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Bonnie Berger
Jul 9, 2011·Nucleic Acids Research·Andrew H Babiskin, Christina D Smolke
Aug 17, 2012·Cell Cycle·Ivan Garcia-Bassets, Dong Wang

Citations

Dec 19, 2012·Journal of the American Chemical Society·Rui WangMinkui Luo
Oct 4, 2013·Database : the Journal of Biological Databases and Curation·Izabella KrystkowiakMichal Dabrowski
Apr 5, 2013·Genome Research·Eugenia Giannopoulou, Olivier Elemento
Feb 26, 2014·BMC Genomics·Dario StrbenacJean Y H Yang
Nov 2, 2012·Genome Biology·Yogesh SaletoreChristopher E Mason
Feb 4, 2014·PloS One·Evangeline W CornwellRobert W Jackman
May 9, 2014·Bioinformatics·Nishanth Ulhas NairPhilipp Bucher
Sep 28, 2014·BMC Research Notes·Krzysztof ChojnowskiMichal Mikula
Nov 22, 2014·Nature Communications·Dimple ChakravartyMark A Rubin
Jan 24, 2013·The Journal of Biological Chemistry·Mack Y SuPatrick G Gallagher
Dec 17, 2014·The Journal of Investigative Dermatology·Xiaoling ZhangJennifer Y Zhang
May 16, 2013·Genes to Cells : Devoted to Molecular & Cellular Mechanisms·Ryuichiro NakatoKatsuhiko Shirahige
Mar 26, 2016·Briefings in Bioinformatics·Vahid JaliliMarco Masseroli
Sep 1, 2015·Cell·Claudio R AlarcónSohail F Tavazoie
Apr 22, 2015·Nature Communications·Heng PanOlivier Elemento
Apr 1, 2015·The Journal of Experimental Medicine·Katerina HatziShane Crotty
Mar 25, 2015·Nature·Claudio R AlarcónSohail F Tavazoie
Aug 23, 2016·PeerJ·Georgios Georgiou, Simon J van Heeringen
Oct 7, 2016·Epigenetics & Chromatin·SriGanesh Jammula, Diego Pasini
Jan 18, 2018·Nature Communications·Matt TeaterRita Shaknovich
May 30, 2019·Genome Research·Severin BergerErik van Nimwegen
Jun 25, 2017·BMC Genomics·Stefano FrattiniPaola Crepaldi
Mar 21, 2017·Proceedings of the National Academy of Sciences of the United States of America·Giulia FabbriRiccardo Dalla-Favera
Dec 2, 2020·Proceedings of the National Academy of Sciences of the United States of America·Mo ZhouMark R Philips
Jan 11, 2017·Cancer Discovery·Jiyuan ZhangLaura Pasqualucci
Oct 14, 2016·Cancer Discovery·Yanwen JiangAri M Melnick
Aug 29, 2014·Cancer Research·Colin J PalmerBoris Reizis

Related Concepts

ETS1 protein, human
Genome Mapping
Enhancer Elements, Genetic
Computer Programs and Programming
Jurkat Cells
Histone Code
Chromatin Immunoprecipitation
Proto-Oncogene Protein c-ets-1
Workflow
High-Throughput Nucleotide Sequencing

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