Improved statistical methods enable greater sensitivity in rhythm detection for genome-wide data

PLoS Computational Biology
Alan L HutchisonAaron R Dinner

Abstract

Robust methods for identifying patterns of expression in genome-wide data are important for generating hypotheses regarding gene function. To this end, several analytic methods have been developed for detecting periodic patterns. We improve one such method, JTK_CYCLE, by explicitly calculating the null distribution such that it accounts for multiple hypothesis testing and by including non-sinusoidal reference waveforms. We term this method empirical JTK_CYCLE with asymmetry search, and we compare its performance to JTK_CYCLE with Bonferroni and Benjamini-Hochberg multiple hypothesis testing correction, as well as to five other methods: cyclohedron test, address reduction, stable persistence, ANOVA, and F24. We find that ANOVA, F24, and JTK_CYCLE consistently outperform the other three methods when data are limited and noisy; empirical JTK_CYCLE with asymmetry search gives the greatest sensitivity while controlling for the false discovery rate. Our analysis also provides insight into experimental design and we find that, for a fixed number of samples, better sensitivity and specificity are achieved with higher numbers of replicates than with higher sampling density. Application of the methods to detecting circadian rhythms in a ...Continue Reading

References

Oct 20, 1975·Biochimica Et Biophysica Acta·B W Matthews
Nov 24, 2001·Neuron·A Claridge-ChangM W Young
Feb 21, 2002·The Journal of Biological Chemistry·Hiroki R UedaSeiichi Hashimoto
Apr 23, 2002·Nature·Kai-Florian StorchCharles J Weitz
May 23, 2002·Cell·Satchidananda PandaJohn B Hogenesch
Jun 29, 2002·Proceedings of the National Academy of Sciences of the United States of America·Yiing LinPaul H Taghert
Jul 12, 2002·American Journal of Human Genetics·B V NorthP C Sham
Jul 12, 2002·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Paul D Etter, Mani Ramaswami
Mar 22, 2003·Current Opinion in Cell Biology·John J TysonBela Novak
Oct 14, 2003·Biochemical Pharmacology·Alfonso PompellaAlessandro F Casini
Apr 9, 2005·Methods in Enzymology·Herman WijnenMichael W Young
May 17, 2005·Genome Biology·Kevin R HayesJohn B Hogenesch
Jun 14, 2005·Nature Reviews. Genetics·Deborah Bell-PedersenMark J Zoran
Mar 29, 2006·Diabetes·Sanjin ZvonicJeffrey M Gimble
Jun 13, 2006·Bioinformatics·S E AhnertT M A Fink
Nov 11, 2006·Annual Review of Genetics·Herman Wijnen, Michael W Young
Feb 7, 2007·Acta Psychiatrica Scandinavica. Supplementum·R Armitage
Mar 31, 2007·Pharmacology & Therapeutics·Colleen A McClung
Apr 14, 2007·Annual Review of Nutrition·Kathryn Moynihan RamseyJoseph Bass
Jun 21, 2007·Genes & Development·Sebastian KadenerMichael Rosbash
Jul 24, 2007·Journal of Physiology, Paris·Urs Albrecht
Sep 4, 2007·Statistical Applications in Genetics and Molecular Biology·Jason MortonBernd Sturmfels
Aug 6, 2008·Human Psychopharmacology·Anne Germain, David J Kupfer
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Jan 20, 2009·Journal of Biological Rhythms·Shin YamazakiMichael Menaker
Aug 4, 2009·PloS One·Louisa A HoovenJadwiga M Giebultowicz
Feb 13, 2010·Annual Review of Physiology·Charna DibnerUrs Albrecht
Mar 30, 2010·Toxicological Sciences : an Official Journal of the Society of Toxicology·Laura Michelle BeaverJadwiga Maria Giebultowicz
Jul 16, 2010·Nature Reviews. Neuroscience·Katharina WulffRussell G Foster
Sep 30, 2010·Journal of Biological Rhythms·Michael E HughesKarl Kornacker
Mar 19, 2011·Cell·Nir Yosef, Aviv Regev
Nov 17, 2011·Genes & Development·Katharine Compton AbruzziMichael Rosbash
Aug 14, 2012·Metallomics : Integrated Biometal Science·Konstantinos Mandilaras, Fanis Missirlis
Jul 5, 2013·Proceedings. Biological Sciences·Osnat BartokSebastian Kadener
Nov 16, 2013·Nucleic Acids Research·Susan E St PierreUNKNOWN FlyBase Consortium
Apr 15, 2014·Theoretical Biology & Medical Modelling·Germaine Cornelissen
May 9, 2014·PloS One·Tomasz ZielinskiAndrew J Millar

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Citations

Nov 4, 2017·Journal of Biological Rhythms·Michael E HughesJohn B Hogenesch
Aug 14, 2018·Journal of Biological Rhythms·Alan L HutchisonAaron R Dinner
Mar 18, 2020·PLoS Computational Biology·David Laloum, Marc Robinson-Rechavi
Jul 17, 2020·Briefings in Bioinformatics·Wenwen MeiYuchao Jiang
Feb 15, 2020·Science·Sandipan RayAkhilesh B Reddy
Nov 27, 2018·Journal of Biological Rhythms·Jordan M Singer, Jacob J Hughey
Mar 21, 2019·Zoological Letters·Hiroyuki J KanayaTaichi Q Itoh
Sep 12, 2018·Proceedings of the National Academy of Sciences of the United States of America·Rosemary BraunRavi Allada
Aug 11, 2020·Computational and Structural Biotechnology Journal·Lingying SunGuang-Zhong Wang
Oct 31, 2020·BMC Bioinformatics·Miha Moškon
Mar 7, 2021·Genes·Vera-Khlara S Oh, Robert W Li
Apr 3, 2021·NAR Genomics and Bioinformatics·Hitoshi Iuchi, Michiaki Hamada
Apr 27, 2021·The Plant Journal : for Cell and Molecular Biology·Gust BilckeKlaas Vandepoele
May 27, 2021·STAR Protocols·Thomas MortimerKevin B Koronowski
Oct 16, 2021·Nature Plants·Xu WangChentao Lin
Sep 9, 2019··Hannah De los SantosKristin P. Bennett
May 14, 2021··Kevin B. KoronowskiSalvador Aznar Benitah

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Software Mentioned

JTK
CYCLE
_ CYCLE
DAVID

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