ECHO: an application for detection and analysis of oscillators identifies metabolic regulation on genome-wide circadian output
Abstract
Abstract Motivation Time courses utilizing genome scale data are a common approach to identifying the biological pathways that are controlled by the circadian clock, an important regulator of organismal fitness. However, the methods used to detect circadian oscillations in these datasets are not able to accommodate changes in the amplitude of the oscillations over time, leading to an underestimation of the impact of the clock on biological systems. Results We have created a program to efficaciously identify oscillations in large-scale datasets, called the Extended Circadian Harmonic Oscillator application, or ECHO. ECHO utilizes an extended solution of the fixed amplitude oscillator that incorporates the amplitude change coefficient. Employing synthetic datasets, we determined that ECHO outperforms existing methods in detecting rhythms with decreasing oscillation amplitudes and in recovering phase shift. Rhythms with changing amplitudes identified from published biological datasets revealed distinct functions from those oscillations that were harmonic, suggesting purposeful biologic regulation to create this subtype of circadian rhythms. Availability and implementation ECHO’s full interface is available at https://github.com/delosh653/ECHO. An R package for this functionality, echo.find, can be downloaded at https://CRAN.R-project.org/package=echo.find. Supplementary information Supplementary data are available at Bioinformatics online.
- Authors:
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1646506
- Grant/Contract Number:
- PNNL 47818
- Resource Type:
- Published Article
- Journal Name:
- Bioinformatics
- Additional Journal Information:
- Journal Name: Bioinformatics Journal Volume: 36 Journal Issue: 3; Journal ID: ISSN 1367-4803
- Publisher:
- Oxford University Press
- Country of Publication:
- United Kingdom
- Language:
- English
Citation Formats
De los Santos, Hannah, Collins, Emily J., Mann, Catherine, Sagan, April W., Jankowski, Meaghan S., Bennett, Kristin P., Hurley, Jennifer M., and Kelso, ed., Janet. ECHO: an application for detection and analysis of oscillators identifies metabolic regulation on genome-wide circadian output. United Kingdom: N. p., 2019.
Web. doi:10.1093/bioinformatics/btz617.
De los Santos, Hannah, Collins, Emily J., Mann, Catherine, Sagan, April W., Jankowski, Meaghan S., Bennett, Kristin P., Hurley, Jennifer M., & Kelso, ed., Janet. ECHO: an application for detection and analysis of oscillators identifies metabolic regulation on genome-wide circadian output. United Kingdom. https://doi.org/10.1093/bioinformatics/btz617
De los Santos, Hannah, Collins, Emily J., Mann, Catherine, Sagan, April W., Jankowski, Meaghan S., Bennett, Kristin P., Hurley, Jennifer M., and Kelso, ed., Janet. Tue .
"ECHO: an application for detection and analysis of oscillators identifies metabolic regulation on genome-wide circadian output". United Kingdom. https://doi.org/10.1093/bioinformatics/btz617.
@article{osti_1646506,
title = {ECHO: an application for detection and analysis of oscillators identifies metabolic regulation on genome-wide circadian output},
author = {De los Santos, Hannah and Collins, Emily J. and Mann, Catherine and Sagan, April W. and Jankowski, Meaghan S. and Bennett, Kristin P. and Hurley, Jennifer M. and Kelso, ed., Janet},
abstractNote = {Abstract Motivation Time courses utilizing genome scale data are a common approach to identifying the biological pathways that are controlled by the circadian clock, an important regulator of organismal fitness. However, the methods used to detect circadian oscillations in these datasets are not able to accommodate changes in the amplitude of the oscillations over time, leading to an underestimation of the impact of the clock on biological systems. Results We have created a program to efficaciously identify oscillations in large-scale datasets, called the Extended Circadian Harmonic Oscillator application, or ECHO. ECHO utilizes an extended solution of the fixed amplitude oscillator that incorporates the amplitude change coefficient. Employing synthetic datasets, we determined that ECHO outperforms existing methods in detecting rhythms with decreasing oscillation amplitudes and in recovering phase shift. Rhythms with changing amplitudes identified from published biological datasets revealed distinct functions from those oscillations that were harmonic, suggesting purposeful biologic regulation to create this subtype of circadian rhythms. Availability and implementation ECHO’s full interface is available at https://github.com/delosh653/ECHO. An R package for this functionality, echo.find, can be downloaded at https://CRAN.R-project.org/package=echo.find. Supplementary information Supplementary data are available at Bioinformatics online.},
doi = {10.1093/bioinformatics/btz617},
journal = {Bioinformatics},
number = 3,
volume = 36,
place = {United Kingdom},
year = {2019},
month = {8}
}
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