Using Lomb-Scargle Periodograms to Identify Periodic Genes in ...

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What is a Periodogram?• A graph showing frequency “power” for a spectrumof frequencies• “Peak” in periodogram indicates a frequency withsignificant periodicityPeriodic SignalPeriodogramLog 2(Expression)ComputationSpectral“Power”TimeFrequency6
Why Lomb-Scargle Instead of Fourier?Lomb-Scargle MethodWeights data pointsData can be unevenly sampledNo data imputationAny number of data pointsKnown statistical properties“p” valueNeed estimate of number of“independent frequencies” butexplore using continuumFourier MethodWeights frequency intervalsRequires uniform spacingMissing data imputed2 N points for FFT; 0 paddingPermutation tests needed toassess statistical propertiesAd hoc scoring rulesUsually only look at“independent” Fourierfrequencies7
Page 1 and 2: Using Lomb-Scargle Periodogramsto I
Page 3: Periodic Patterns in BiologyA verte
Page 8 and 9: Lomb-Scargle PeriodogramExample Usi
Page 10 and 11: Lomb-Scargle PeriodogramExample Usi
Page 12 and 13: Lomb-Scargle Periodogram Experiment
Page 14 and 15: Lomb-Scargle Periodogram Experiment
Page 16 and 17: Lomb-Scargle Experiment:Mixtures: P
Page 18 and 19: Data Pipeline to Apply to Microarra
Page 20 and 21: Bozdech’s Plasmodium dataset:1. A
Page 30 and 31: Bozdech’s Plasmodium dataset:Boze
Page 32 and 33: Mary-Lee’s Somitogenesis DatasetW
Page 34 and 35: Somitogenesis DatasetMary-Lee, Scie
Page 36 and 37: Somitogenesis DatasetDo we care abo
Page 38 and 39: Somitogenesis DatasetPerturbation (
Page 44 and 45: Somitogenesis DatasetWhat periodici
Page 46 and 47: Conclusions• Lomb-Scargle periodo
Page 48: AcknowledgementsPourquie LabOlivier

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