Analysis of computational footprinting methods for DNase sequencing experiments

Nature Methods
Eduardo G GusmaoIvan G Costa

Abstract

DNase-seq allows nucleotide-level identification of transcription factor binding sites on the basis of a computational search of footprint-like DNase I cleavage patterns on the DNA. Frequently in high-throughput methods, experimental artifacts such as DNase I cleavage bias affect the computational analysis of DNase-seq experiments. Here we performed a comprehensive and systematic study on the performance of computational footprinting methods. We evaluated ten footprinting methods in a panel of DNase-seq experiments for their ability to recover cell-specific transcription factor binding sites. We show that three methods-HINT, DNase2TF and PIQ-consistently outperformed the other evaluated methods and that correcting the DNase-seq signal for experimental artifacts significantly improved the accuracy of computational footprints. We also propose a score that can be used to detect footprints arising from transcription factors with potentially short residence times.

References

May 17, 2000·Bioinformatics·G D Stormo
Dec 26, 2001·Nucleic Acids Research·T HubbardM Clamp
Apr 9, 2004·Proceedings of the National Academy of Sciences of the United States of America·Peter J SaboJohn A Stamatoyannopoulos
Nov 20, 2004·Proceedings of the National Academy of Sciences of the United States of America·Peter J SaboJohn A Stamatoyannopoulos
Jul 19, 2005·Genome Research·Adam SiepelDavid Haussler
Dec 31, 2005·Nucleic Acids Research·V MatysE Wingender
Sep 14, 2006·Journal of Cell Science·Z Dave SharpMichael A Mancini
Sep 12, 2008·Bioinformatics·Alan P BoyleTerrence S Furey
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Mar 17, 2009·BMC Bioinformatics·Bartek WilczynskiJerzy Tiuryn
Mar 24, 2009·Nature Methods·Jay R HesselberthJohn A Stamatoyannopoulos
Sep 9, 2009·Nature Reviews. Genetics·Peter J Park
Sep 24, 2009·Bioinformatics·Janne KorhonenEsko Ukkonen
Jan 8, 2010·The Journal of Biological Chemistry·Cécile E MalnouIsabelle Jariel-Encontre
Jan 25, 2011·Nature Genetics·Sam JohnJohn A Stamatoyannopoulos
Feb 19, 2011·Bioinformatics·Charles E GrantWilliam Stafford Noble
Nov 11, 2011·Bioinformatics·Gabriel Cuellar-PartidaTimothy L Bailey
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Sep 8, 2012·Nature·Shane NephJohn A Stamatoyannopoulos
Apr 12, 2013·Proceedings of the National Academy of Sciences of the United States of America·Allan LazaroviciHarmen J Bussemaker
May 28, 2013·Cell Reports·Hirotaka NakahashiRafael Casellas
Nov 1, 2013·Proceedings of the National Academy of Sciences of the United States of America·Leonid TeytelmanAlexander van Oudenaarden
Sep 17, 2014·Nature Reviews. Genetics·Clifford A Meyer, X Shirley Liu
Sep 23, 2014·Molecular Cell·Myong-Hee SungGordon L Hager
Oct 9, 2014·Nucleic Acids Research·Galip Gürkan YardımcıUwe Ohler
Nov 21, 2014·Nature·Andrew B StergachisJohn A Stamatoyannopoulos
Jan 22, 2015·Nucleic Acids Research·Matthew E RitchieGordon K Smyth
May 26, 2015·Nature Methods

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Citations

May 23, 2017·Nature Reviews. Genetics·Olivier Cuvier, Beat Fierz
Apr 27, 2016·Current Opinion in Biotechnology·Deborah ChasmanSushmita Roy
May 5, 2017·Nucleic Acids Research·Tim KehlHans-Peter Lenhof
Nov 11, 2017·Nucleic Acids Research·André L MartinsMichael J Guertin
Dec 21, 2018·Genome Research·Hongyang LiYuanfang Guan
Aug 8, 2018·Bioinformatics·Florian Schmidt, Marcel H Schulz
Apr 12, 2019·PloS One·Ravi MadduriIan Foster
Nov 22, 2018·Briefings in Bioinformatics·Tianlei XuHao Wu
Nov 18, 2018·Nucleic Acids Research·Ivan YevshinFedor Kolpakov
Feb 28, 2019·Genome Biology·Zhijian LiIvan G Costa
Jul 17, 2018·Briefings in Bioinformatics·Yongjing LiuMing Chen
Jun 24, 2017·PLoS Computational Biology·Rasmus MagnussonMika Gustafsson
May 20, 2020·Genome Research·Luca MarianiMartha L Bulyk
Apr 6, 2018·Journal of the Royal Society, Interface·Travers ChingCasey S Greene
Oct 9, 2019·Nature Neuroscience·Ilaria PalmisanoSimone Di Giovanni
Feb 6, 2020·Genome Biology·Feng YanNicholas C Wong
Feb 8, 2020·Epigenetics & Chromatin·Florian SchmidtMarcel H Schulz
Oct 17, 2018·Scientific Reports·Zhen ShenDe-Shuang Huang
May 31, 2020·BMC Bioinformatics·Elisabetta SautaRiccardo Bellazzi
May 26, 2017·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Ido Goldstein, Gordon L Hager
Jun 6, 2019·Epigenetics & Chromatin·Kyu-Seon OhMyong-Hee Sung
Oct 10, 2020·Nature Communications·Kristin E MurphyPatrick J Murphy
Oct 31, 2020·Nucleic Acids Research·Fan WangChunquan Li
Sep 23, 2020·Genome Génome / Conseil National De Recherches Canada·Ian C TobiasJennifer A Mitchell
Nov 15, 2020·Science Advances·Andrew B CaldwellShankar Subramaniam
May 1, 2021·International Journal of Molecular Sciences·Costantino ParisiCecilia Lanny Winata
Oct 31, 2017·Current Opinion in Systems Biology·Deborah Chasman, Sushmita Roy

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