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Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

Authors
Mark Gerstein,Zhi Lu
Eric Nostrand,Chao Cheng,Bradley Arshinoff,Tao Liu,Kevin Yip,R. Robilotto,Andreas Rechtsteiner,Kohta Ikegami,Pedro Alves,Aurélien Chateigner,Marc Perry,Mitzi Morris,Raymond Auerbach,Hui Yang,Jing Leng,Anne Vielle,Wei Niu,Kahn Rhrissorrakrai,Ashish Agarwal,Roger Alexander,Galt Barber,Cathleen Brdlik,Jennifer Brennan,Jeremy Brouillet,Adrian Carr,Ming Cheung,Hiram Clawson,Sergio Contrino,Luke Dannenberg,Abby Dernburg,Arshad Desai,Lindsay Dick,Andrea Dosé,Jiang Du,Thea Egelhofer,Sevinç Ercan,Ghia Euskirchen,Brent Ewing,Elise Feingold,Reto Gassmann,Peter Good,Phil Green,F. Gullier,Michelle Gutwein,Mark Guyer,Lukas Habegger,Ting Han,Steven Henikoff,Stefan Henz,Angie Hinrichs,H. Holster,Anthony Hyman,Al Iniguez,J. Janette,Morten Jensen,Masaomi Kato,W. Kent,Ellen Kephart,Vishal Khivansara,Ekta Khurana,John Kim,Paulina Kolasinska-Zwierz,Eric Lai,Isabel Latorre,Amber Leahey,Suzanna Lewis,Paul Lloyd,Lucas Lochovsky,Rebecca Lowdon,Yaniv Lubling,Rachel Lyne,Michael MacCoss,Sebastian Mackowiak,Marco Mangone,Sheldon McKay,Desirea Mecenas,Gennifer Merrihew,David Miller,Andrew Muroyama,John Murray,Siew Ooi,Vu Pham,T. Phippen,Elicia Preston,Nikolaus Rajewsky,Gunnar Rätsch,Heidi Rosenbaum,Joel Rozowsky,Kim Rutherford,Peter Ruzanov,Mihail Sarov,Rajkumar Sasidharan,Andrea Sboner,Paul Scheid,Eran Segal,Hyunjin Shin,Chong Shou,Frank Slack,C. Slightam,Richard Smith,W. Spencer,Eo Stinson,S. Taing,Teruaki Takasaki,Dionne Vafeados,K. Voronina,Guilin Wang,Nicole Washington,Christina Whittle,Beijing Wu,Koon-Kiu Yan,Georg Zeller,Zheng Zha,Mei Zhong,Xingliang Zhou,Julie Ahringer,Susan Strome,Kristin Gunsalus,Gos Micklem,Xuyuan Liu,V Reinke,Stuart Kim,LaDeana Hillier,Fabio Piano,M Snyder,Lincoln Stein,Jason Lieb,R Waterston
+128 authors
,D. Mecenas
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Published
Dec 23, 2010
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Abstract

We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor-binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.

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