methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles
Altuna Akalin,Matthias Kormaksson,Sheng Li,Francine E. Garrett-Bakelman,Maria E. Figueroa,Ari Melnick,Christopher E. Mason +6 more
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TLDR
An R package that rapidly analyzes genome-wide cytosine epigenetic profiles from high-throughput methylation and Hydroxymethylation sequencing experiments is described, which includes functions for clustering, sample quality visualization, differential methylation analysis and annotation features, thus automating and simplifying many of the steps for discerning statistically significant bases or regions of DNAmethylation.Abstract:
DNA methylation is a chemical modification of cytosine bases that is pivotal for gene regulation, cellular specification and cancer development. Here, we describe an R package, methylKit, that rapidly analyzes genome-wide cytosine epigenetic profiles from high-throughput methylation and hydroxymethylation sequencing experiments. methylKit includes functions for clustering, sample quality visualization, differential methylation analysis and annotation features, thus automating and simplifying many of the steps for discerning statistically significant bases or regions of DNA methylation. Finally, we demonstrate methylKit on breast cancer data, in which we find statistically significant regions of differential methylation and stratify tumor subtypes. methylKit is available at http://code.google.com/p/methylkit.read more
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Next-generation characterization of the Cancer Cell Line Encyclopedia
Mahmoud Ghandi,Franklin W. Huang,Franklin W. Huang,Franklin W. Huang,Judit Jané-Valbuena,Judit Jané-Valbuena,Gregory V. Kryukov,Christopher Lo,E. Robert McDonald,Jordi Barretina,Ellen Gelfand,Craig M. Bielski,Haoxin Li,Haoxin Li,Kevin Hu,Alexander Y. Andreev-Drakhlin,Jaegil Kim,Julian M. Hess,Brian J. Haas,François Aguet,Barbara A. Weir,Michael V. Rothberg,Brenton R. Paolella,Michael S. Lawrence,Rehan Akbani,Yiling Lu,Hong L. Tiv,Prafulla C. Gokhale,Antoine de Weck,Ali Amin Mansour,Coyin Oh,Juliann Shih,Kevin Hadi,Yanay Rosen,Jonathan Bistline,Kavitha Venkatesan,Anupama Reddy,Dmitriy Sonkin,Dmitriy Sonkin,Manway Liu,Joseph Lehar,Joshua M. Korn,Dale Porter,Michael D. Jones,Javad Golji,Giordano Caponigro,Jordan E. Taylor,Caitlin M. Dunning,Amanda L. Creech,Allison Warren,James M. McFarland,Mahdi Zamanighomi,Audrey Kauffmann,Nicolas Stransky,Marcin Imielinski,Yosef E. Maruvka,Yosef E. Maruvka,Andrew D. Cherniack,Andrew D. Cherniack,Aviad Tsherniak,Francisca Vazquez,Jacob D. Jaffe,Andrew A. Lane,David M. Weinstock,Cory M. Johannessen,Michael Morrissey,Frank Stegmeier,Robert Schlegel,William C. Hahn,William C. Hahn,Gad Getz,Gordon B. Mills,Jesse S. Boehm,Todd R. Golub,Todd R. Golub,Todd R. Golub,Levi A. Garraway,Levi A. Garraway,William R. Sellers,William R. Sellers +79 more
TL;DR: The original Cancer Cell Line Encyclopedia is expanded with deeper characterization of over 1,000 cell lines, including genomic, transcriptomic, and proteomic data, and integration with drug-sensitivity and gene-dependency data, which reveals potential targets for cancer drugs and associated biomarkers.
Journal ArticleDOI
Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome
Boulos Chalhoub,Shengyi Liu,Isobel A. P. Parkin,Haibao Tang,Haibao Tang,Xiyin Wang,Julien Chiquet,Harry Belcram,Chaobo Tong,Birgit Samans,Margot Correa,Corinne Da Silva,Jérémy Just,Cyril Falentin,Chu Shin Koh,Isabelle Le Clainche,Maria Bernard,Pascal Bento,Benjamin Noel,Karine Labadie,Adriana Alberti,Mathieu Charles,Dominique Arnaud,Hui Guo,Christian Daviaud,Salman Alamery,Kamel Jabbari,Kamel Jabbari,Meixia Zhao,Patrick P. Edger,Houda Chelaifa,David C. Tack,Gilles Lassalle,Imen Mestiri,Nicolas Schnel,Marie-Christine Le Paslier,Guangyi Fan,Victor Renault,Philippe E. Bayer,Agnieszka A. Golicz,Sahana Manoli,Tae-Ho Lee,Vinh Ha Dinh Thi,Smahane Chalabi,Qiong Hu,Chuchuan Fan,Reece Tollenaere,Yunhai Lu,Christophe Battail,Jinxiong Shen,Christine Sidebottom,Xinfa Wang,Aurélie Canaguier,Aurélie Chauveau,Aurélie Bérard,G. Deniot,Mei Guan,Zhongsong Liu,Fengming Sun,Yong Pyo Lim,Eric Lyons,Christopher D. Town,Ian Bancroft,Xiaowu Wang,Jinling Meng,Jianxin Ma,J. Chris Pires,Graham J.W. King,Dominique Brunel,Régine Delourme,Michel Renard,Jean-Marc Aury,Keith L. Adams,Jacqueline Batley,Jacqueline Batley,Rod J. Snowdon,Jörg Tost,David Edwards,David Edwards,Yongming Zhou,Wei Hua,Andrew G. Sharpe,Andrew H. Paterson,Chunyun Guan,Patrick Wincker,Patrick Wincker,Patrick Wincker +86 more
TL;DR: The polyploid genome of Brassica napus, which originated from a recent combination of two distinct genomes approximately 7500 years ago and gave rise to the crops of rape oilseed, is sequenced.
Journal ArticleDOI
Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer
Himisha Beltran,Himisha Beltran,Davide Prandi,Juan Miguel Mosquera,Juan Miguel Mosquera,Matteo Benelli,Loredana Puca,Joanna Cyrta,Clarisse Marotz,Eugenia G. Giannopoulou,Balabhadrapatruni V. S. K. Chakravarthi,Sooryanarayana Varambally,Scott A. Tomlins,David M. Nanus,Scott T. Tagawa,Eliezer M. Van Allen,Eliezer M. Van Allen,Olivier Elemento,Olivier Elemento,Andrea Sboner,Andrea Sboner,Levi A. Garraway,Levi A. Garraway,Levi A. Garraway,Mark A. Rubin,Mark A. Rubin,Francesca Demichelis,Francesca Demichelis,Francesca Demichelis +28 more
TL;DR: Analysis of whole-exome sequencing data of metastatic biopsies from patients observed substantial genomic overlap between castration-resistant tumors that were histologically characterized as prostate adenocarcinomas and neuroendocrine prostate cancer (CRPC-NE), supporting the emergence of an alternative, 'AR-indifferent' cell state through divergent clonal evolution as a mechanism of treatment resistance in advanced prostate cancer.
Journal ArticleDOI
Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
TL;DR: Sailfish, a computational method for quantifying the abundance of previously annotated RNA isoforms from RNA-seq data, exemplifies the potential of lightweight algorithms for efficiently processing sequencing reads.
Journal ArticleDOI
The transcriptional landscape of polyploid wheat
Ricardo H. Ramirez-Gonzalez,Philippa Borrill,Daniel Lang,Sophie A. Harrington,Jemima Brinton,Luca Venturini,Mark W. Davey,John Jacobs,F. van Ex,Asher Pasha,Yogendra Khedikar,Stephen J. Robinson,Aron T. Cory,Tobin Florio,Lorenzo Concia,Caroline Juery,Henk-jan Schoonbeek,Burkhard Steuernagel,Daoquan Xiang,Christopher J. Ridout,Boulos Chalhoub,Klaus F. X. Mayer,Moussa Benhamed,David Latrasse,Abdelhafid Bendahmane,Brande B. H. Wulff,Rudi Appels,Vijay K. Tiwari,Raju Datla,Frédéric Choulet,Curtis J. Pozniak,Nicholas J. Provart,Andrew G. Sharpe,Etienne Paux,Manuel Spannagl,Andrea Bräutigam,Cristobal Uauy +36 more
TL;DR: This study leverages 850 wheat RNA-sequencing samples, alongside the annotated genome, to determine the similarities and differences between homoeolog expression across a range of tissues, developmental stages, and cultivars and suggests that the transposable elements in promoters relate more closely to the variation in the relative expression of homoeologicals across tissues than to a ubiquitous effect across all tissues.
References
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