Guidelines for Genome-Scale Analysis of Biological Rhythms.

TitleGuidelines for Genome-Scale Analysis of Biological Rhythms.
Publication TypeJournal Article
Year of Publication2017
AuthorsHughes ME, Abruzzi KC, Allada R, Anafi R, Arpat ABulak, Asher G, Baldi P, de Bekker C, Bell-Pedersen D, Blau J, Brown S, M Ceriani F, Chen Z, Chiu JC, Cox J, Crowell AM, DeBruyne JP, Dijk D-J, DiTacchio L, Doyle FJ, Duffield GE, Dunlap JC, Eckel-Mahan K, Esser KA, FitzGerald GA, Forger DB, Francey LJ, Fu Y-H, Gachon F, Gatfield D, de Goede P, Golden SS, Green C, Harer J, Harmer S, Haspel J, Hastings MH, Herzel H, Herzog ED, Hoffmann C, Hong C, Hughey JJ, Hurley JM, de la Iglesia HO, Johnson C, Kay SA, Koike N, Kornacker K, Kramer A, Lamia K, Leise T, Lewis SA, Li J, Li X, Liu AC, Loros JJ, Martino TA, Menet JS, Merrow M, Millar AJ, Mockler T, Naef F, Nagoshi E, Nitabach MN, Olmedo M, Nusinow DA, Ptáček LJ, Rand D, Reddy AB, Robles MS, Roenneberg T, Rosbash M, Ruben MD, Rund SSC, Sancar A, Sassone-Corsi P, Sehgal A, Sherrill-Mix S, Skene DJ, Storch K-F, Takahashi JS, Ueda HR, Wang H, Weitz C, Westermark PO, Wijnen H, Xu Y, Wu G, Yoo S-H, Young M, Zhang EErquan, Zielinski T, Hogenesch JB
JournalJ Biol Rhythms
Volume32
Issue5
Pagination380-393
Date Published2017 Oct
ISSN1552-4531
Abstract

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.

DOI10.1177/0748730417728663
Alternate JournalJ. Biol. Rhythms
PubMed ID29098954
PubMed Central IDPMC5692188
Grant ListR01 GM114424 / GM / NIGMS NIH HHS / United States
R01 GM112991 / GM / NIGMS NIH HHS / United States
R01 NS094211 / NS / NINDS NIH HHS / United States
R01 GM063911 / GM / NIGMS NIH HHS / United States
R01 GM107434 / GM / NIGMS NIH HHS / United States
R01 AG045795 / AG / NIA NIH HHS / United States
R35 GM118022 / GM / NIGMS NIH HHS / United States
U01 EB021956 / EB / NIBIB NIH HHS / United States
R01 GM111387 / GM / NIGMS NIH HHS / United States
R35 GM124685 / GM / NIGMS NIH HHS / United States
U54 NS083932 / NS / NINDS NIH HHS / United States
R01 AG045828 / AG / NIA NIH HHS / United States
U01 EB022546 / EB / NIBIB NIH HHS / United States
R01 GM087508 / GM / NIGMS NIH HHS / United States
U54 HD083211 / HD / NICHD NIH HHS / United States
P30 AG028740 / AG / NIA NIH HHS / United States
R21 AR069266 / AR / NIAMS NIH HHS / United States
P30 ES013508 / ES / NIEHS NIH HHS / United States
U19 AI116491 / AI / NIAID NIH HHS / United States
R01 GM069418 / GM / NIGMS NIH HHS / United States
R01 NS095367 / NS / NINDS NIH HHS / United States
R01 NS091070 / NS / NINDS NIH HHS / United States
R01 GM113673 / GM / NIGMS NIH HHS / United States
R01 NS054794 / NS / NINDS NIH HHS / United States
R01 GM098931 / GM / NIGMS NIH HHS / United States
R35 GM118290 / GM / NIGMS NIH HHS / United States
R01 GM104991 / GM / NIGMS NIH HHS / United States
/ / Wellcome Trust / United Kingdom
R35 GM118021 / GM / NIGMS NIH HHS / United States
R01 DK097164 / DK / NIDDK NIH HHS / United States
R01 GM102225 / GM / NIGMS NIH HHS / United States
SC1 GM109861 / GM / NIGMS NIH HHS / United States

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