Strengths and limitations of period estimation methods for circadian data

PLoS ONE

Volumn 9, Issue 5, 2014, Pages

  Zielinski, Tomasz ^a   Moore, Anne M ^a   Troup, Eilidh ^a   Halliday, Karen J ^a   Millar, Andrew J ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BIOLOGICAL DATA REPOSITORY; CIRCADIAN RHYTHM; CONTROLLED STUDY; CURVE FITTING; DATA ANALYSIS; ENRIGHT PERIODOGRAM; INFORMATION SERVICE; INFORMATION SYSTEM; INTERMETHOD COMPARISON; LOMB SCARGLE PERIODOGRAM; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; MAXIMUM ENTROPY SPECTRAL ANALYSIS; NON LINEAR LEAST SQUARES; QUANTITATIVE ANALYSIS; SPECTRUM RESAMPLING; ALGORITHM; COMPARATIVE STUDY; HUMAN; PERIODICITY; PHYSIOLOGY; THEORETICAL MODEL;

ALGORITHMS; CIRCADIAN RHYTHM; HUMANS; MODELS, THEORETICAL; PERIODICITY;

EID: 84901507275     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0096462     Document Type: Article

References (41)

1. Mackey SR, Golden SS (2007) Winding up the cyanobacterial circadian clock. Trends in Microbiology 15 (9): 381-388. (Pubitemid 47375111)
2. Dong G, Golden SS (2008) How a cyanobacterium tells time. Current Opinion in Microbiology 11 (6): 541-546.
3. Ukai H, Ueda HR (2010) Systems Biology of Mammalian Circadian Clocks. Annual Review of Physiology 72: 579-603.
4. Lowrey PL, Takahashi JS (2011) Genetics of Circadian Rhythms in Mammaliam Model Organisms. Advances in Genetics 74: 175-229.
5. Ishiura M, Kutsuna S, Aoki S, Iwasaki H, Andersson CR, et al. (1998) Expression of a Gene Cluster kaiABC as a Circadian Feedback Process. Cyanobacteria Science 281: 1519-1523. (Pubitemid 28425578)
6. Millar AJ, Carre IA, Strayer CA, Chua N, Kay SA (1995) Circadian clock mutants in Arabidopsis identified by luciferase imaging. Science 267 (5201): 1161-1163.
7. Zhang EE, Liu AC, Hirota T, Miraglia LJ, Welch G, et al. (2009) A genomewide RNAi screen for modifiers of the circadian clock in human cells. Cell 139: 199-210.
8. Maier B, Wendt S, Vanselow JT, Wallach T, Reischl S, et al. (2009) A large-scale functional RNAi screen reveals a role for CK2 in the mammalian circadian clock. Genes Dev. 23: 708-718.
9. Straume M, Frasier-Cadoret SG, Johnson ML (1991) Least Squares Analysis of Fluorescence Data. In: Lakowicz JR editor. Topics in Fluorescence Spectroscopy, Volume 2: Plenum. pp 117-240.
10. Enright JT (1965) The search for rhythmicity in Biological Time-series. J. Theoret Biol. 8: 426-268
11. Lomb NR (1976) Least-squares frequency analysis of unequally spaced data. Astrophys. Space Sci. 39: 447-462.
12. Edwards KD, Akman OE, Knox K, Lumsden PJ, Thomson AW, et al. (2010) Quantitative analysis of regulatory flexibility under changing environmental conditions. Molecular Systems Biology, 6: 424.
13. Burg JP (1972) The relationship between maximum entropy spectra and maximum likelihood spectra. Geophysics 37: 375-376.
14. Costa MJ, Finkenstädt B, Roche V, Lévi F, Gould PD, et al. (2013) Inference on periodicity of circadian time series. Biostatistics: 1-15.
15. Moore A, Zielinski T, Millar AJ (2014) Online Period Estimation and Determination of Rhythmicity in Circadian Data Using the BioDare Data Infrastructure, In: Staiger D. Plant Circadian Networks: Methods and Protocols. Methods in Molecular Biology Series: Humana Press. in press.
16. Refinetti R (2004) Non-stationary time series and the robustness of circadian rhythms. Journal Theoretical Biology 227: 571-581.
17. Refinetti R (1992) Laboratory instrumentation and computing: comparison of six methods for the determination of the period of circadian rhythms. Physiology & Behaviour 54: 869-875.
18. Lichtenberg U, Jensen LJ, Fausbøll A, Jensen TS, Bork P, et al. (2005) Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics 21(7): 1191-1201. (Pubitemid 41762882)
19. Sokolove PG, Bushell WN (1978) The Chi Square Periodogram: Its Utility for Analysis of Circadian Rhythms. J. Theor. Biol. 72: 131-160. (Pubitemid 8350595)
20. Johnson M (2010) Essential Numerical Computer Methods. Elsevier.
21. Johnson ML, Frasier SG (1985) Nonlinear Least Squares Analysis. Methods Enzymol 117: 301-342.
22. Bloomfield P (2000) Fourier Analysis of Time Series: An Introduction. Oxford: Wiley-Blackwell.
23. Dowse HB, Ringo JM (1989) The Search for Hidden Periodicities in Biological Time Series Revisited. J. Theor. Biol. 139: 487-515.
24. Trancart T, Lambert P, Rochard E, Daverat F, Coustillas J, et al. (2012) Alternative flood tide transport tact in caradromous speciese: Anguilla anguilla, Liza ramada and Platichthys flesus. Estuarine Coastal and Shelf Science 99: 191-198.
25. Darnell MZ, Rittschof D, Forward, Richard B (2010) Endogenous swimming rhythms underlying the spawning migration of the blue crab, Callinectes sapidus: ontogeny and variation with ambient tidal regime. Marine Biology 157(11): 2415-2425.
26. Halberg F, Tong YL, Johnson EA (1967) Circadian system phase, an aspect of temporal morphology: procedures and illustrative examples. In: Mayersbach H, editor. The Cellular Aspects of Biorhythms. Berlin: Springer. pp 20-48.
27. Leise TL, Harrington ME (2011) Wavelet-Based Time Series Analysis of Circadian Rhythms. J. Biol Rhythms 26: 454-463.
28. Price TS, Baggs JE, Curtis AM, FitzGerald GA, Hogenesch JB (2008) WAVECLOCK: Wavelet analysis of circadian oscillation. Bioinformatics 24(23): 2794-2795. (Pubitemid 352722632)
29. Bretthorst GL (1988) Bayesian Spectrum Analysis and Parameter Estimation, Lecture Notes in Statistics, 48: Springer-Verlag.
30. Cohen AL, Leise TL, Welsh DK (2012) Bayesian statistical analysis of circadian oscillations in fibroblasts. J. Theor. Biol. 314: 182-191.
31. Locke JCW, Southern MM, Kozma-Bognar L, Hibberd V, Brown PE, et al. (2005) Extension of a genetic network model by iterative experimentation and mathematical analysis. Molecular Systems Biology 1:13.
32. Southern MM, Millar AJ (2005) Circadian genetics in the model higher plant, Arabidopsis thaliana. Methods Enzymol 393: 23-35. (Pubitemid 40486519)
33. Goldbeter A (1991) A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase, PNAS 88: 9107-9111.
34. Monk NAM (2003) Oscillatory expression of Hes1, p53 and NF-κB driven by transcriptional time delays. Current Biology 13: 1409-1413.
35. Heron EA, Finkenstädt B, Rand DA (2007) Bayesian inference for dynamic transcriptional regulation: the hes1 system as a case study. Bioinformatics 23: 2596-2603. (Pubitemid 350048363)
36. Gould PD, Locke JC, Larue C, Southern MM, Davis SJ, et al. (2006) The molecular basis of temperature compensation in the Arabidopsis circadian clock. Plant Cell 18: 1177-1187. (Pubitemid 43956124)
37. Dowse HB (2013) Maximum entropy spectral analysis for circadian rhythms: theory, history and practice. J. Circ. Rhythms 11:6.
38. Andersen N (1974) On the calculation of filter coefficients for maximum entropy spectral analysis. Geophys. 39: 69-72.
39. Barrodale I, Erickson RE (1980) Algorithms for least-squares linear prediction and maximum entropy spectral analysis. Geophysics 45: 420-432. (Pubitemid 10468792)
40. Glynn EF, Chen J, Mushegian AR (2006) Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodogram. Bioinformatics 22: 310-316. (Pubitemid 43205377)
41. Hughes ME, DiTacchio L, Hayes KR, Vollmers C, Pulivarthy S, et al. (2009) Harmonics of Circadian Gene Transcription in Mammals. PLoS Genet 5(4): e1000442.