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These patterns are clues to discovering genes implicated in cellcycle, circadian, and other periodic biological processes. The algorithm, implemented in a program called ENRAGE (Entropy-based Rhythmic Analysis of Gene Expression), treats the task of estimating an expression profile's periodicity and phase as a simultaneous bicriterion optimization problem. Specifically, a frequency domain spectrum is reconstructed from a time-series of gene expression data, subject to two constraints: (a) the likelihood of the spectrum and (b) the Shannon entropy of the reconstructed spectrum.
These patterns are clues to discovering rhythmic genes implicated in cell-cycle, circadian, or other biological processes. The algorithm, implemented in a program called rage (Rhythmic Analysis of Gene Expression), decouples the problems of estimating a pattern's periodicity and phase. Our algorithm is linear-time in frequency and phase resolution, an improvement over previous quadratic-time approaches.