Extended Circadian Harmonic Oscillators (ECHO)

Extended Circadian Harmonic Oscillators (ECHO) detects oscillatory patterns in large-scale time-course biological datasets by modeling amplitude changes to characterize circadian, ultradian, and infradian rhythms.

Key Features:

• Extended Harmonic Oscillator Model: ECHO employs an extended solution of the fixed-amplitude oscillator model that incorporates a coefficient for amplitude change to identify oscillations with varying amplitudes.
• Performance on synthetic datasets: Evaluations using synthetic datasets show improved detection of rhythms with decreasing amplitudes and accurate recovery of phase shifts.
• Biological insight into amplitude changes: Identification of rhythms with changing amplitudes in published biological datasets reveals distinct functional subclasses of circadian oscillations and suggests regulatory roles of the circadian clock.
• Integration with PAICE and R: ECHO is part of the PAICE (Pipeline for Amplitude Integration of Circadian Exploration) Suite and is implemented in R for statistical analysis.

Scientific Applications:

• Genomic and systems biology: Applies to time-course genomic datasets to identify temporally regulated genes and pathways driven by circadian and other rhythmic processes.
• Metabolic and pathway analysis: Detects rhythm amplitude changes and phase dynamics relevant to metabolic regulation and pathway-level temporal organization.

Methodology:

Uses an extended harmonic oscillator model with an amplitude-change coefficient; performance assessed on synthetic datasets with recovery of phase shifts; implemented in R and integrated into the PAICE suite.