Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang,Tao Liu,Clifford A. Meyer,Jérôme Eeckhoute,David S. Johnson,Bradley E. Bernstein,Bradley E. Bernstein,Chad Nusbaum,Richard M. Myers,Myles Brown,Wei Li,X. Shirley Liu +11 more
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TLDR
This work presents Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer, and uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions.Abstract:
We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available.read more
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A comparative encyclopedia of DNA elements in the mouse genome
Feng Yue,Feng Yue,Yong Cheng,Alessandra Breschi,Jeff Vierstra,Weisheng Wu,Weisheng Wu,Tyrone Ryba,Tyrone Ryba,Richard Sandstrom,Zhihai Ma,Carrie A. Davis,Benjamin D. Pope,Yin Shen,Dmitri D. Pervouchine,Sarah Djebali,Robert E. Thurman,Rajinder Kaul,Eric Rynes,Anthony Kirilusha,Georgi K. Marinov,Brian A. Williams,Diane Trout,Henry Amrhein,Katherine I. Fisher-Aylor,Igor Antoshechkin,Gilberto DeSalvo,Lei Hoon See,Meagan Fastuca,Jorg Drenkow,Chris Zaleski,Alexander Dobin,Pablo Prieto,Julien Lagarde,Giovanni Bussotti,Andrea Tanzer,Olgert Denas,Kanwei Li,M. A. Bender,M. A. Bender,Miaohua Zhang,Rachel Byron,Mark Groudine,Mark Groudine,David McCleary,Long Pham,Zhen Ye,Samantha Kuan,Lee Edsall,Yi-Chieh Wu,Matthew D. Rasmussen,Mukul S. Bansal,Manolis Kellis,Manolis Kellis,Cheryl A. Keller,Christapher S. Morrissey,Tejaswini Mishra,Deepti Jain,Nergiz Dogan,Robert S. Harris,Philip Cayting,Trupti Kawli,Alan P. Boyle,Alan P. Boyle,Ghia Euskirchen,Anshul Kundaje,Shin Lin,Yiing Lin,Camden Jansen,Venkat S. Malladi,Melissa S. Cline,Drew T. Erickson,Vanessa M. Kirkup,Katrina Learned,Cricket A. Sloan,Kate R. Rosenbloom,Beatriz Lacerda de Sousa,Kathryn Beal,Miguel Pignatelli,Paul Flicek,Jin Lian,Tamer Kahveci,Dongwon Lee,W. James Kent,Miguel Santos,Javier Herrero,Cedric Notredame,Audra K. Johnson,Shinny Vong,Kristen Lee,Daniel Bates,Fidencio Neri,Morgan Diegel,Theresa K. Canfield,Peter J. Sabo,Matthew S. Wilken,Thomas A. Reh,Erika Giste,Anthony Shafer,Tanya Kutyavin,Eric Haugen,Douglas Dunn,Alex Reynolds,Shane Neph,Richard Humbert,R. Scott Hansen,Marella F. T. R. de Bruijn,Licia Selleri,Alexander Y. Rudensky,Steven Z. Josefowicz,Robert M. Samstein,Evan E. Eichler,Stuart H. Orkin,Dana N. Levasseur,Thalia Papayannopoulou,Kai Hsin Chang,Arthur I. Skoultchi,Srikanta Gosh,Christine M. Disteche,Piper M. Treuting,Yanli Wang,Mitchell J. Weiss,Gerd A. Blobel,Xiaoyi Cao,Sheng Zhong,Ting Wang,Peter J. Good,Rebecca F. Lowdon,Rebecca F. Lowdon,Leslie B. Adams,Leslie B. Adams,Xiao Qiao Zhou,Michael J. Pazin,Elise A. Feingold,Barbara J. Wold,James Taylor,Ali Mortazavi,Sherman M. Weissman,John A. Stamatoyannopoulos,Michael Snyder,Roderic Guigó,Thomas R. Gingeras,David M. Gilbert,Ross C. Hardison,Michael A. Beer,Bing Ren +145 more
TL;DR: By comparing with the human genome, this work not only confirms substantial conservation in the newly annotated potential functional sequences, but also finds a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization.
Journal ArticleDOI
Tissue-Specific Mitotic Bookmarking by Hematopoietic Transcription Factor GATA1
Stephan Kadauke,Maheshi Udugama,Jan M. Pawlicki,Jordan C. Achtman,Deepti Jain,Yong Cheng,Ross C. Hardison,Gerd A. Blobel,Gerd A. Blobel +8 more
TL;DR: A requirement of mitotic "bookmarking" by GATA1 for the faithful propagation of cell-type-specific transcription programs through cell division is suggested.
Journal ArticleDOI
Activation of the Glucocorticoid Receptor Is Associated with Poor Prognosis in Estrogen Receptor-Negative Breast Cancer
TL;DR: Gene expression analysis revealed that ER(-) tumors expressing high GR levels exhibited differential activation of EMT, cell adhesion, and inflammation pathways, suggesting a direct transcriptional role for GR in determining the outcome of poor-prognosis ER(+) breast cancers.
Journal ArticleDOI
Fine Tuning of Craniofacial Morphology by Distant-Acting Enhancers
Catia Attanasio,Alexander Nord,Yiwen Zhu,Matthew J. Blow,Zirong Li,Denise K. Liberton,Harris Morrison,Ingrid Plajzer-Frick,Amy Holt,Roya Hosseini,Sengthavy Phouanenavong,Jennifer A. Akiyama,Malak Shoukry,Veena Afzal,Edward M. Rubin,Edward M. Rubin,David R. FitzPatrick,David R. FitzPatrick,Bing Ren,Benedikt Hallgrímsson,Benedikt Hallgrímsson,Len A. Pennacchio,Len A. Pennacchio,Axel Visel,Axel Visel +24 more
TL;DR: The results support that variation in the sequence or copy number of craniofacial enhancers may contribute to the spectrum of facial variation the authors find in human populations.
Journal ArticleDOI
Recurrent somatic mutations in POLR2A define a distinct subset of meningiomas
Victoria E. Clark,Akdes Serin Harmanci,Hanwen Bai,Mark W. Youngblood,Tong Ihn Lee,Jacob F Baranoski,A. Gulhan Ercan-Sencicek,Brian J. Abraham,Abraham S. Weintraub,Denes Hnisz,Matthias Simon,Boris Krischek,E. Zeynep Erson-Omay,Octavian Henegariu,Geneive Carrión-Grant,Ketu Mishra-Gorur,Daniel Duran,Johanna Goldmann,Johannes Schramm,Roland Goldbrunner,Joseph M. Piepmeier,Alexander O. Vortmeyer,Jennifer Moliterno Günel,Kaya Bilguvar,Katsuhito Yasuno,Richard A. Young,Murat Gunel +26 more
TL;DR: In this paper, a combination of next-generation genomic analyses of 775 meningiomas was used to identify a role for essential transcriptional machinery in driving tumorigenesis.
References
More filters
Journal ArticleDOI
High-resolution profiling of histone methylations in the human genome.
Artem Barski,Suresh Cuddapah,Kairong Cui,Tae-Young Roh,Dustin E. Schones,Zhibin Wang,Gang Wei,Iouri Chepelev,Keji Zhao +8 more
TL;DR: High-resolution maps for the genome-wide distribution of 20 histone lysine and arginine methylations as well as histone variant H2A.Z, RNA polymerase II, and the insulator binding protein CTCF across the human genome using the Solexa 1G sequencing technology are generated.
Journal ArticleDOI
Global variation in copy number in the human genome
Richard Redon,Shumpei Ishikawa,Karen R. Fitch,Lars Feuk,George H. Perry,T. Daniel Andrews,Heike Fiegler,Michael H. Shapero,Andrew R. Carson,Wenwei Chen,Eun Kyung Cho,Stephanie Dallaire,Jennifer L. Freeman,Juan R. González,Mònica Gratacòs,Jing Huang,Dimitrios Kalaitzopoulos,Daisuke Komura,Jeffrey R. MacDonald,Christian R. Marshall,Rui Mei,Lyndal Montgomery,Keunihiro Nishimura,Kohji Okamura,Fan Shen,Martin J. Somerville,Joelle Tchinda,Armand Valsesia,Cara Woodwark,Fengtang Yang,Junjun Zhang,Tatiana Zerjal,Jane Zhang,Lluís Armengol,Donald F. Conrad,Xavier Estivill,Chris Tyler-Smith,Nigel P. Carter,Hiroyuki Aburatani,Charles Lee,Keith W. Jones,Stephen W. Scherer,Matthew E. Hurles +42 more
TL;DR: A first-generation CNV map of the human genome is constructed through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia, underscoring the importance of CNV in genetic diversity and evolution and the utility of this resource for genetic disease studies.
Journal ArticleDOI
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Tarjei S. Mikkelsen,Manching Ku,Manching Ku,David B. Jaffe,Biju Issac,Biju Issac,Erez Lieberman Aiden,Erez Lieberman Aiden,Georgia Giannoukos,Pablo Alvarez,William Brockman,Tae Kyung Kim,Richard Koche,Richard Koche,Richard Koche,William Lee,Eric M. Mendenhall,Eric M. Mendenhall,Aisling O'Donovan,Aviva Presser,Carsten Russ,Xiaohui Xie,Alexander Meissner,Marius Wernig,Rudolf Jaenisch,Chad Nusbaum,Eric S. Lander,Eric S. Lander,Bradley E. Bernstein,Bradley E. Bernstein +29 more
TL;DR: The application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells is reported and it is shown that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms.
Journal ArticleDOI
Genome-Wide Mapping of in Vivo Protein-DNA Interactions
David S. Johnson,Ali Mortazavi,Ali Mortazavi,Richard M. Myers,Richard M. Myers,Barbara J. Wold,Barbara J. Wold +6 more
TL;DR: A large-scale chromatin immunoprecipitation assay based on direct ultrahigh-throughput DNA sequencing was developed, which was then used to map in vivo binding of the neuron-restrictive silencer factor (NRSF; also known as REST) to 1946 locations in the human genome.
PatentDOI
Genome-wide location and function of dna binding proteins
TL;DR: In this paper, a method for identifying a set of genes where cell cycle regulator binding correlates with gene expression and identifying genomic targets of cell cycle transcription activators in living cells is also encompassed.