Guidelines for Genome-Scale Analysis of Biological Rhythms

Article Article scientifique Article Guidelines for Genome-Scale Analysis of Biological Rhythms eng 2017-11-03 2017-11-03 author Hughes Michael E. Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA author Abruzzi Katherine C. Department of Biology and Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts, USA author Allada Ravi Department of Neurobiology, Northwestern University, Evanston, Illinois, USA author Anafi Ron Division of Sleep Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA author Arpat Alaaddin Bulak 0000-0002-7749-3793 Center for Integrative Genomics, Génopode, University of Lausanne, Lausanne, Switzerland author Asher Gad 0000-0001-9403-7856 Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel 640349 author Baldi Pierre Institute for Genomics and Bioinformatics, University of California, Irvine, USA author de Bekker Charissa 0000-0002-7325-172X Department of Biology, University of Central Florida, Orlando, USA author Bell-Pedersen Deborah 0000-0002-1639-8215 Department of Biology, Texas A&M University, College Station, USA author Blau Justin Department of Biology, New York University, New York, USA author Brown Steve Institute of Pharmacology and Toxicology, University of Zürich, Switzerland author Ceriani M. Fernanda Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina author Chen Zheng 0000-0001-8829-7504 Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, Houston, USA author Chiu Joanna C. Department of Entomology and Nematology, University of California, Davis, USA author Cox Juergen Computational Systems Biochemistry, Max-Planck Institute of Biochemistry, Martinsried, Germany author Crowell Alexander M. Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA author DeBruyne Jason P. Department of Pharmacology and Toxicology, Morehouse School of Medicine, Atlanta, Georgia, USA author Dijk Derk-Jan 0000-0001-5314-1008 Surrey Sleep Research Centre, University of Surrey, Guildford, UK author DiTacchio Luciano The University of Kansas Medical Center, University of Kansas, Kansas City, USA author Doyle Francis J. John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, Massachusetts, USA author Duffield Giles E. Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA author Dunlap Jay C. Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA author Eckel-Mahan Kristin Institute of Molecular Medicine, McGovern Medical School, UT Health Houston, Houston, Texas, USA author Esser Karyn A. Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, USA author FitzGerald Garret A. Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA author Forger Daniel B. Department of Mathematics, University of Michigan, Ann Arbor, USA author Francey Lauren J. Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA author Fu Ying-Hui Kavli Institute for Fundamental Neuroscience, Weill Institute of Neuroscience, Department of Neurology, University of California, San Francisco, USA author Gachon Frédéric Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, Lausanne, Switzerland 543253 author Gatfield David 0000-0001-5114-2824 Center for Integrative Genomics, Génopode, University of Lausanne, Lausanne, Switzerland 602037 author de Goede Paul Department of Endocrinology & Metabolism, Academic Medical Center, Amsterdam, the Netherlands author Golden Susan S. Center for Circadian Biology and Division of Biological Sciences, University of California, San Diego, La Jolla, USA author Green Carla Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, USA author Harer John Department of Mathematics, Duke University, Durham, North Carolina, USA author Harmer Stacey Department of Plant Biology, University of California, Davis, USA author Haspel Jeff Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA author Hastings Michael H. Medical Research Council Laboratory of Molecular Biology, Cambridge, UK author Herzel Hanspeter Institute for Theoretical Biology, Charité-Universitätsmedizin Berlin, Germany author Herzog Erik D. Department of Biology, Washington University in St. Louis, Missouri, USA author Hoffmann Christy 0000-0003-1855-3693 Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA author Hong Christian Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA author Hughey Jacob J. Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA author Hurley Jennifer M. Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA author de la Iglesia Horacio O. Department of Biology, University of Washington, Seattle, USA author Johnson Carl Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA author Kay Steve A. Department of Cell and Molecular Biology, The Scripps Research Institute, University of California, San Diego, La Jolla, USA author Koike Nobuya Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Japan author Kornacker Karl Division of Sensory Biophysics, The Ohio State University, Columbus, USA author Kramer Achim 0000-0001-9671-6078 Laboratory of Chronobiology, Charité Universitätsmedizin Berlin, Germany author Lamia Katja Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA author Leise Tanya Department of Mathematics and Statistics, Amherst College, Amherst, Massachusetts, USA author Lewis Scott A. Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA author Li Jiajia Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA 760350 author Li Xiaodong Department of Cell Biology, College of Life Sciences at Wuhan University, China author Liu Andrew C. Department of Biological Sciences, University of Memphis, Tennessee, USA author Loros Jennifer J. Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA author Martino Tami A. Centre for Cardiovascular Investigations, Department of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada author Menet Jerome S. Department of Biology, Texas A&M University, College Station, USA author Merrow Martha Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Germany author Millar Andrew J. SynthSys and School of Biological Sciences, University of Edinburgh, UK author Mockler Todd Donald Danforth Plant Science Center, St. Louis, Missouri, USA author Naef Felix 0000-0001-9786-3037 The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland author Nagoshi Emi 0000-0002-6365-4074 Department of Genetics and Evolution, University of Geneva, Switzerland 535940 Département de génétique et évolution (Genev) (BIANI) author Nitabach Michael N. Department of Cellular and Molecular Physiology, Department of Genetics, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, Connecticut, USA author Olmedo Maria 0000-0002-5701-2665 Department of Genetics, University of Seville, Spain author Nusinow Dmitri A. Donald Danforth Plant Science Center, St. Louis, Missouri, USA author Ptáček Louis J. Department of Neurology, University of California, San Francisco, USA author Rand David Warwick Systems Biology and Mathematics Institute, University of Warwick, Conventry, UK author Reddy Akhilesh B. The Francis Crick Institute, London, UK, and UCL Institute of Neurology, Queen Square, London, UK author Robles Maria S. Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Germany author Roenneberg Till 0000-0003-2939-0332 Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Germany author Rosbash Michael 0000-0003-3366-1780 Department of Biology and Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts, USA author Ruben Marc D. Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA author Rund Samuel S. C. Centre for Immunity, Infection and Evolution, University of Edinburgh, UK author Sancar Aziz Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, USA author Sassone-Corsi Paolo Department of Biological Chemistry, Center for Epigenetics and Metabolism, University of California, Irvine, USA author Sehgal Amita Howard Hughes Medical Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA author Sherrill-Mix Scott 0000-0002-8955-8072 Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA author Skene Debra J. Chronobiology, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK author Storch Kai-Florian Department of Psychiatry, Douglas Mental Health University Institute, McGill University, Montreal, Canada author Takahashi Joseph S. Howard Hughes Medical Institute, Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, USA author Ueda Hiroki R. Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Osaka, Japan author Wang Han 0000-0003-2420-3147 Center for Circadian Clocks, Soochow University, Suzhou, Jiangsu, China 411597 author Weitz Charles Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA author Westermark Pål O. Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany author Wijnen Herman 0000-0002-8710-5176 Biological Sciences and Institute for Life Sciences, University of Southampton, UK author Xu Ying 0000-0002-6689-7768 Cam-Su GRC, Soochow University, Suzhou, China 903100 author Wu Gang Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA author Yoo Seung-Hee Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, Houston, USA author Young Michael Laboratory of Genetics, Rockefeller University, New York, New York, USA author Zhang Eric Erquan 0000-0002-4472-7493 National Institute of Biological Sciences, Beijing, China author Zielinski Tomasz 0000-0002-0194-5706 SynthSys and School of Biological Sciences, University of Edinburgh, UK author Hogenesch John B. Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA 380-393 10.1177/0748730417728663 29098954 0748-7304 PMC5692188 http://journals.sagepub.com/doi/10.1177/0748730417728663 <p>Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods hold significant promise for future discovery, particularly when combined with computational modeling. However, genome-scale experiments are costly and laborious, yielding “big data” that are conceptually and statistically difficult to analyze. There is no obvious consensus regarding design or analysis. Here we discuss the relevant technical considerations to generate reproducible, statistically sound, and broadly useful genome-scale data. Rather than suggest a set of rigid rules, we aim to codify principles by which investigators, reviewers, and readers of the primary literature can evaluate the suitability of different experimental designs for measuring different aspects of biological rhythms. We introduce CircaInSilico, a web-based application for generating synthetic genome biology data to benchmark statistical methods for studying biological rhythms. Finally, we discuss several unmet analytical needs, including applications to clinical medicine, and suggest productive avenues to address them.</p> ChIP-seq RNA-seq Biostatistics Circadian rhythms Computational biology Diurnal rhythms Functional genomics Guidelines Metabolomics Proteomics Systems biology Dewey 590 Biotechnology and Biological Sciences Research Council BB/I019405/1 Medical Research Council MC_U105170643 NIGMS NIH HHS R01 GM098931 NINDS NIH HHS R01 NS054794 NIBIB NIH HHS U01 EB021956 NICHD NIH HHS U54 HD083211 NIA NIH HHS P30 AG028740 NIDDK NIH HHS R01 DK097164 NIAMS NIH HHS R01 AR066082 NIEHS NIH HHS P30 ES013508 NIAID NIH HHS U19 AI116491 Wellcome Trust Integrating metabolic and transcriptional circadian clocks. 100333 Molecular Basis of Cell Function 44 Département de génétique et évolution 162 false Journal of biological rhythms 32 5 a5520bee-ead6-476b-ac1e-5b8427037130 Article (Published version) Public Article-scientifique-from-unpaywall.pdf 518915 application/pdf CC BY 7203b4b72211ac95b4019918c1f6775bbb6e8c98ccf9deaaaf46dc0e31ea88cf openAccess Faculté des sciences / Section de biologie / Département de génétique et évolution

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Gatfield, David