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Guidelines for Genome-Scale Analysis of Biological Rhythms

Hughes, Michael E., Abruzzi, Katherine C., Allada, Ravi, Anafi, Ron, Arpat, Alaaddin Bulak, Asher, Gad, Baldi, Pierre, de Bekker, Charissa, Bell-Pedersen, Deborah, Blau, Justin , Brown, Steve, Ceriani, M. Fernanda, Chen, Zheng, Chiu, Joanna C., Cox, Juergen, Crowell, Alexander M., DeBruyne, Jason P., Dijk, Derk-Jan, DiTacchio, Luciano, Doyle, Francis J., Duffield, Giles E., Dunlap, Jay C., Eckel-Mahan, Kristin, Esser, Karyn A., FitzGerald, Garret A., Forger, Daniel B., Francey, Lauren J., Fu, Ying-Hui, Gachon, Frédéric, Gatfield, David, de Goede, Paul, Golden, Susan S., Green, Carla, Harer, John, Harmer, Stacey, Haspel, Jeff, Hastings, Michael H., Herzel, Hanspeter, Herzog, Erik D., Hoffmann, Christy, Hong, Christian, Hughey, Jacob J., Hurley, Jennifer M., de la Iglesia, Horacio O., Johnson, Carl, Kay, Steve A., Koike, Nobuya, Kornacker, Karl, Kramer, Achim, Lamia, Katja, Leise, Tanya, Lewis, Scott A., Li, Jiajia, Li, Xiaodong, Liu, Andrew C., Loros, Jennifer J., Martino, Tami A., Menet, Jerome S., Merrow, Martha, Millar, Andrew J., Mockler, Todd, Naef, Felix, Nagoshi, Emi, Nitabach, Michael N., Olmedo, Maria, Nusinow, Dmitri A., Ptáček, Louis J., Rand, David, Reddy, Akhilesh B., Robles, Maria S., Roenneberg, Till, Rosbash, Michael, Ruben, Marc D., Rund, Samuel S.C., Sancar, Aziz, Sassone-Corsi, Paolo, Sehgal, Amita, Sherrill-Mix, Scott, Skene, Debra, Storch, Kai-Florian, Takahashi, Joseph S., Ueda, Hiroki R., Wang, Han, Weitz, Charles, Westermark, Pål O., Wijnen, Herman, Xu, Ying, Wu, Gang, Yoo, Seung-Hee, Young, Michael, Zhang, Eric Erquan, Zielinski, Tomasz and Hogenesch, John B. (2017) Guidelines for Genome-Scale Analysis of Biological Rhythms Journal of Biological Rhythms, 32 (5). pp. 380-393.

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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.

Item Type: Article
Divisions : Faculty of Health and Medical Sciences > School of Biosciences and Medicine
Authors :
NameEmailORCID
Hughes, Michael E.
Abruzzi, Katherine C.
Allada, Ravi
Anafi, Ron
Arpat, Alaaddin Bulak
Asher, Gad
Baldi, Pierre
de Bekker, Charissa
Bell-Pedersen, Deborah
Blau, Justin
Brown, Steve
Ceriani, M. Fernanda
Chen, Zheng
Chiu, Joanna C.
Cox, Juergen
Crowell, Alexander M.
DeBruyne, Jason P.
Dijk, Derk-JanD.J.Dijk@surrey.ac.uk
DiTacchio, Luciano
Doyle, Francis J.
Duffield, Giles E.
Dunlap, Jay C.
Eckel-Mahan, Kristin
Esser, Karyn A.
FitzGerald, Garret A.
Forger, Daniel B.
Francey, Lauren J.
Fu, Ying-Hui
Gachon, Frédéric
Gatfield, David
de Goede, Paul
Golden, Susan S.
Green, Carla
Harer, John
Harmer, Stacey
Haspel, Jeff
Hastings, Michael H.
Herzel, Hanspeter
Herzog, Erik D.
Hoffmann, Christy
Hong, Christian
Hughey, Jacob J.
Hurley, Jennifer M.
de la Iglesia, Horacio O.
Johnson, Carl
Kay, Steve A.
Koike, Nobuya
Kornacker, Karl
Kramer, Achim
Lamia, Katja
Leise, Tanya
Lewis, Scott A.
Li, Jiajia
Li, Xiaodong
Liu, Andrew C.
Loros, Jennifer J.
Martino, Tami A.
Menet, Jerome S.
Merrow, Martha
Millar, Andrew J.
Mockler, Todd
Naef, Felix
Nagoshi, Emi
Nitabach, Michael N.
Olmedo, Maria
Nusinow, Dmitri A.
Ptáček, Louis J.
Rand, David
Reddy, Akhilesh B.
Robles, Maria S.
Roenneberg, Till
Rosbash, Michael
Ruben, Marc D.
Rund, Samuel S.C.
Sancar, Aziz
Sassone-Corsi, Paolo
Sehgal, Amita
Sherrill-Mix, Scott
Skene, DebraD.Skene@surrey.ac.uk
Storch, Kai-Florian
Takahashi, Joseph S.
Ueda, Hiroki R.
Wang, Han
Weitz, Charles
Westermark, Pål O.
Wijnen, Herman
Xu, Ying
Wu, Gang
Yoo, Seung-Hee
Young, Michael
Zhang, Eric Erquan
Zielinski, Tomasz
Hogenesch, John B.
Date : 3 November 2017
Identification Number : 10.1177/0748730417728663
Copyright Disclaimer : © 2017 The Author(s). Published under a CC-BY license.
Uncontrolled Keywords : Circadian rhythms; Diurnal rhythms; Computational biology; Functional genomics; Systems biology; Guidelines; Biostatistics; RNA-seq; ChIP-seq; Proteomics; Metabolomics
Depositing User : Clive Harris
Date Deposited : 09 Nov 2017 12:12
Last Modified : 14 Mar 2018 15:32
URI: http://epubs.surrey.ac.uk/id/eprint/844874

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