Guidelines for Genome-Scale Analysis of Biological Rhythms
Creators: name: Rund, Samuel S.C.
name: Zhang, Eric Erquan
name: Sancar, Aziz
name: DiTacchio, Luciano
name: Blau, Justin
name: Li, Jiajia
name: Hastings, Michael H.
name: Allada, Ravi
name: de la Iglesia, Horacio O.
name: Wu, Gang
name: Duffield, Giles E.
name: Haspel, Jeff
name: Chen, Zheng
name: Menet, Jerome S.
name: Wang, Han
name: Dijk, Derk-Jan
name: Ptáček, Louis J.
name: Crowell, Alexander M.
name: Liu, Andrew C.
name: Ueda, Hiroki R.
name: Chiu, Joanna C.
name: Weitz, Charles
name: Ceriani, M. Fernanda
name: Merrow, Martha
name: Sehgal, Amita
name: Arpat, Alaaddin Bulak
name: Leise, Tanya
name: Koike, Nobuya
name: Herzel, Hanspeter
name: Hoffmann, Christy
name: Forger, Daniel B.
name: Francey, Lauren J.
name: Doyle, Francis J.
name: Nitabach, Michael N.
name: Westermark, Pål O.
name: Naef, Felix
name: Abruzzi, Katherine C.
name: Takahashi, Joseph S.
name: Rand, David
name: Hughes, Michael E.
name: Anafi, Ron
name: Dunlap, Jay C.
name: Hughey, Jacob J.
name: Eckel-Mahan, Kristin
name: Harmer, Stacey
name: FitzGerald, Garret A.
name: DeBruyne, Jason P.
name: Loros, Jennifer J.
name: Ruben, Marc D.
name: Kay, Steve A.
name: Asher, Gad
name: Kornacker, Karl
name: Sherrill-Mix, Scott
name: Robles, Maria S.
name: de Goede, Paul
name: Cox, Juergen
name: Nusinow, Dmitri A.
name: Li, Xiaodong
name: Johnson, Carl
name: Lamia, Katja
name: Wijnen, Herman
name: Sassone-Corsi, Paolo
name: Olmedo, Maria
name: Young, Michael
name: Herzog, Erik D.
name: Gatfield, David
name: Green, Carla
name: Gachon, Frédéric
name: Bell-Pedersen, Deborah
name: Brown, Steve
name: Storch, Kai-Florian
name: Hogenesch, John B.
name: de Bekker, Charissa
name: Millar, Andrew J.
name: Roenneberg, Till
name: Esser, Karyn A.
name: Hong, Christian
name: Reddy, Akhilesh B.
name: Kramer, Achim
name: Mockler, Todd
name: Rosbash, Michael
name: Nagoshi, Emi
name: Fu, Ying-Hui
name: Skene, Debra J.
name: Yoo, Seung-Hee
name: Lewis, Scott A.
name: Golden, Susan S.
name: Hurley, Jennifer M.
name: Zielinski, Tomasz
name: Harer, John
name: Martino, Tami A.
name: Baldi, Pierre
name: Xu, Ying
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: 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.