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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.

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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.UNSPECIFIEDUNSPECIFIED
Abruzzi, Katherine C.UNSPECIFIEDUNSPECIFIED
Allada, RaviUNSPECIFIEDUNSPECIFIED
Anafi, RonUNSPECIFIEDUNSPECIFIED
Arpat, Alaaddin BulakUNSPECIFIEDUNSPECIFIED
Asher, GadUNSPECIFIEDUNSPECIFIED
Baldi, PierreUNSPECIFIEDUNSPECIFIED
de Bekker, CharissaUNSPECIFIEDUNSPECIFIED
Bell-Pedersen, DeborahUNSPECIFIEDUNSPECIFIED
Blau, JustinUNSPECIFIEDUNSPECIFIED
Brown, SteveUNSPECIFIEDUNSPECIFIED
Ceriani, M. FernandaUNSPECIFIEDUNSPECIFIED
Chen, ZhengUNSPECIFIEDUNSPECIFIED
Chiu, Joanna C.UNSPECIFIEDUNSPECIFIED
Cox, JuergenUNSPECIFIEDUNSPECIFIED
Crowell, Alexander M.UNSPECIFIEDUNSPECIFIED
DeBruyne, Jason P.UNSPECIFIEDUNSPECIFIED
Dijk, Derk-JanD.J.Dijk@surrey.ac.ukUNSPECIFIED
DiTacchio, LucianoUNSPECIFIEDUNSPECIFIED
Doyle, Francis J.UNSPECIFIEDUNSPECIFIED
Duffield, Giles E.UNSPECIFIEDUNSPECIFIED
Dunlap, Jay C.UNSPECIFIEDUNSPECIFIED
Eckel-Mahan, KristinUNSPECIFIEDUNSPECIFIED
Esser, Karyn A.UNSPECIFIEDUNSPECIFIED
FitzGerald, Garret A.UNSPECIFIEDUNSPECIFIED
Forger, Daniel B.UNSPECIFIEDUNSPECIFIED
Francey, Lauren J.UNSPECIFIEDUNSPECIFIED
Fu, Ying-HuiUNSPECIFIEDUNSPECIFIED
Gachon, FrédéricUNSPECIFIEDUNSPECIFIED
Gatfield, DavidUNSPECIFIEDUNSPECIFIED
de Goede, PaulUNSPECIFIEDUNSPECIFIED
Golden, Susan S.UNSPECIFIEDUNSPECIFIED
Green, CarlaUNSPECIFIEDUNSPECIFIED
Harer, JohnUNSPECIFIEDUNSPECIFIED
Harmer, StaceyUNSPECIFIEDUNSPECIFIED
Haspel, JeffUNSPECIFIEDUNSPECIFIED
Hastings, Michael H.UNSPECIFIEDUNSPECIFIED
Herzel, HanspeterUNSPECIFIEDUNSPECIFIED
Herzog, Erik D.UNSPECIFIEDUNSPECIFIED
Hoffmann, ChristyUNSPECIFIEDUNSPECIFIED
Hong, ChristianUNSPECIFIEDUNSPECIFIED
Hughey, Jacob J.UNSPECIFIEDUNSPECIFIED
Hurley, Jennifer M.UNSPECIFIEDUNSPECIFIED
de la Iglesia, Horacio O.UNSPECIFIEDUNSPECIFIED
Johnson, CarlUNSPECIFIEDUNSPECIFIED
Kay, Steve A.UNSPECIFIEDUNSPECIFIED
Koike, NobuyaUNSPECIFIEDUNSPECIFIED
Kornacker, KarlUNSPECIFIEDUNSPECIFIED
Kramer, AchimUNSPECIFIEDUNSPECIFIED
Lamia, KatjaUNSPECIFIEDUNSPECIFIED
Leise, TanyaUNSPECIFIEDUNSPECIFIED
Lewis, Scott A.UNSPECIFIEDUNSPECIFIED
Li, JiajiaUNSPECIFIEDUNSPECIFIED
Li, XiaodongUNSPECIFIEDUNSPECIFIED
Liu, Andrew C.UNSPECIFIEDUNSPECIFIED
Loros, Jennifer J.UNSPECIFIEDUNSPECIFIED
Martino, Tami A.UNSPECIFIEDUNSPECIFIED
Menet, Jerome S.UNSPECIFIEDUNSPECIFIED
Merrow, MarthaUNSPECIFIEDUNSPECIFIED
Millar, Andrew J.UNSPECIFIEDUNSPECIFIED
Mockler, ToddUNSPECIFIEDUNSPECIFIED
Naef, FelixUNSPECIFIEDUNSPECIFIED
Nagoshi, EmiUNSPECIFIEDUNSPECIFIED
Nitabach, Michael N.UNSPECIFIEDUNSPECIFIED
Olmedo, MariaUNSPECIFIEDUNSPECIFIED
Nusinow, Dmitri A.UNSPECIFIEDUNSPECIFIED
Ptáček, Louis J.UNSPECIFIEDUNSPECIFIED
Rand, DavidUNSPECIFIEDUNSPECIFIED
Reddy, Akhilesh B.UNSPECIFIEDUNSPECIFIED
Robles, Maria S.UNSPECIFIEDUNSPECIFIED
Roenneberg, TillUNSPECIFIEDUNSPECIFIED
Rosbash, MichaelUNSPECIFIEDUNSPECIFIED
Ruben, Marc D.UNSPECIFIEDUNSPECIFIED
Rund, Samuel S.C.UNSPECIFIEDUNSPECIFIED
Sancar, AzizUNSPECIFIEDUNSPECIFIED
Sassone-Corsi, PaoloUNSPECIFIEDUNSPECIFIED
Sehgal, AmitaUNSPECIFIEDUNSPECIFIED
Sherrill-Mix, ScottUNSPECIFIEDUNSPECIFIED
Skene, DebraD.Skene@surrey.ac.ukUNSPECIFIED
Storch, Kai-FlorianUNSPECIFIEDUNSPECIFIED
Takahashi, Joseph S.UNSPECIFIEDUNSPECIFIED
Ueda, Hiroki R.UNSPECIFIEDUNSPECIFIED
Wang, HanUNSPECIFIEDUNSPECIFIED
Weitz, CharlesUNSPECIFIEDUNSPECIFIED
Westermark, Pål O.UNSPECIFIEDUNSPECIFIED
Wijnen, HermanUNSPECIFIEDUNSPECIFIED
Xu, YingUNSPECIFIEDUNSPECIFIED
Wu, GangUNSPECIFIEDUNSPECIFIED
Yoo, Seung-HeeUNSPECIFIEDUNSPECIFIED
Young, MichaelUNSPECIFIEDUNSPECIFIED
Zhang, Eric ErquanUNSPECIFIEDUNSPECIFIED
Zielinski, TomaszUNSPECIFIEDUNSPECIFIED
Hogenesch, John B.UNSPECIFIEDUNSPECIFIED
Date : 2017
Identification Number : 10.1177/0748730417728663
Copyright Disclaimer : © 2017 The Author(s)
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 : 09 Nov 2017 12:12
URI: http://epubs.surrey.ac.uk/id/eprint/844874

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