MetaCycle: an integrated R package to evaluate periodicity in large scale data

Wu, Gang; Anafi, Ron C.; Hughes, Michael; Kornacker, Karl; Hogenesch, John B.

doi:10.1093/bioinformatics/btw405

Cited by 470 publications

(438 citation statements)

References 12 publications

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“…ARSER detrends data and then detects rhythmic signals with a period between 20 and 28 hours through a combination of autoregressive spectral analysis (alternative to the classical fast Fourier transformation) and harmonic regression (sinusoidal fits) and then reports relevant parameters such as period, phase, and amplitude along with significance statistics. ARSER was run through the MetaCycle package implemented in R (Wu et al., 2016). ARSER has been shown to frequently perform better than other popular circadian gene identification algorithms when analyzing data collected over two days with 4-hour resolution (Wu et al, 2016; Yang and Su, 2010).…”

Section: Star Methodsmentioning

confidence: 99%

“…ARSER was run through the MetaCycle package implemented in R (Wu et al., 2016). ARSER has been shown to frequently perform better than other popular circadian gene identification algorithms when analyzing data collected over two days with 4-hour resolution (Wu et al, 2016; Yang and Su, 2010). Cutoffs of p<0.05 and Benjamini and Hochberg false-discovery rate (FDR) <0.20 were used to identify circadian transcripts.…”

Section: Star Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Acid Suspends the Circadian Clock in Hypoxia through Inhibition of mTOR

Walton

Patel

Brooks

et al. 2018

Cell

195

165

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Summary: Recent reports ind icate hypoxia influences the circadian clock through the transcriptional activities of hypoxia inducible factors (HIFs) at clock genes. Unexpectedly, we uncover a profound disruption of the circadian clock and diurnal transcriptome when hypoxic cells are permitted to acidify, recapitulating the tumor microenvironment. Buffering against acidification or inhibiting lactic acid production fully rescues circadian oscillation. Acidification of several human and murine cell lines, as well as primary murine T cells, suppresses mechanistic target of rapamycin complex 1 (mTORC1) signaling, a key regulator of translation in response to metabolic status. We find acid drives peripheral redistribution of normally perinuclear lysosomes away from perinuclear RHEB, inhibiting lysosome-bound mTOR activity. Restoring mTORC1 signaling and the translation it governs rescues clock oscillation, revealing a model in which acid produced during the cellular metabolic response to hypoxia suppresses the circadian clock through diminished translation of clock constituents.

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Section: Star Methodsmentioning

confidence: 99%

Section: Star Methodsmentioning

confidence: 99%

Acid Suspends the Circadian Clock in Hypoxia through Inhibition of mTOR

Walton

Patel

Brooks

et al. 2018

Cell

195

165

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“…p<0.05 was considered significant. JTK Cycle was used as described (Wu et al, 2016). The program cosinor was downloaded from www.Circadian.org (last accessed 09/01/2016).…”

Section: Methodsmentioning

confidence: 99%

Desoxycorticosterone pivalate‐salt treatment leads to non‐dipping hypertension in Per1 knockout mice

et al. 2016

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Aim Increasing evidence demonstrates that circadian clock proteins are important regulators of physiological functions including blood pressure. An established risk factor for developing cardiovascular disease is the absence of a blood pressure dip during the inactive period. The goal of the present study was to determine the effects of a high salt diet plus mineralocorticoid on PER1-mediated blood pressure regulation in a salt-resistant, normotensive mouse model, C57BL/6J. Methods Blood pressure was measured using radiotelemetry. After control diet, wild type and Per1 knockout mice were given a high salt diet (4% NaCl) and the long-acting mineralocorticoid deoxycorticosterone pivalate. Blood pressure and activity rhythms were analyzed to evaluate changes over time. Results Blood pressure in wild type mice was not affected by a high salt diet plus mineralocorticoid. In contrast, Per1 knockout mice exhibited significantly increased mean arterial pressure in response to a high salt diet plus mineralocorticoid. The inactive/active phase ratio of mean arterial pressure in wild type mice was unchanged by high salt plus mineralocorticoid treatment. Importantly, this treatment caused Per1 knockout mice to lose the expected decrease or “dip” in blood pressure during the inactive compared to the active phase. Conclusion Loss of PER1 increased sensitivity to the high salt plus mineralocorticoid treatment. Italso resulted in a non-dipper phenotype in this model of salt-sensitive hypertension and provides a unique model of non-dipping. Together these data support an important role for the circadian clock protein PER1 in the modulation of blood pressure in a high salt/mineralocorticoid model of hypertension.

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“…There have been steady developments in software to extract rhythmic signals from the non-rhythmic background; these are now highly developed and in passing a few technical issues should be noted. There are more stringent (JTK, 92, 93) and less stringent (ARSER, 94)) software and algorithms available for calling rhythmic genes. To be dependably able to call rhythmic genes sampling density must be high; samples taken at least every 2 hrs over 2 days are needed to reliably identify even 80% of rhythmic genes, and hourly sampling is better (92).…”

Section: Output From the Clockmentioning

confidence: 99%

Making Time: Conservation of Biological Clocks from Fungi to Animals

2017

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SUMMARY The capacity for biological timekeeping arose at least three times through evolution, in prokaryotic cyanobacteria, in cells that evolved into higher plants, and within the group of organisms that eventually became the Fungi and the Animals. Neurospora is a tractable model system for understanding the molecular bases of circadian rhythms in the last of these groups, and is perhaps the most intensively studied circadian cell type. Rhythmic processes described in fungi include growth rate, stress responses, developmental capacity and sporulation as well as much of metabolism; fungi use clocks to anticipate daily environmental changes. A negative feedback loop comprises the core of the circadian system in fungi and animals. In Neurospora, the best studied fungal model, it is driven by two transcription factors, WC-1 and WC-2, that form the White Collar Complex (WCC). WCC elicits expression of the frq gene. FRQ complexes with other proteins, physically interacts with the WCC, and reduces its activity; the kinetics of these processes is strongly influenced by progressive phosphorylation of FRQ. When FRQ become sufficiently phosphorylated that it loses the ability to influence WCC activity the circadian cycle starts again. Environmental cycles of light and temperature influence frq and FRQ expression and thereby reset the internal circadian clocks. The molecular basis of circadian output is also becoming understood. Taken together, molecular explanations are emerging for all the canonical circadian properties, providing a molecular and regulatory framework that may be extended to many members of the Fungal and Animal kingdoms, including humans.

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MetaCycle: an integrated R package to evaluate periodicity in large scale data

Cited by 470 publications

References 12 publications

Acid Suspends the Circadian Clock in Hypoxia through Inhibition of mTOR

Acid Suspends the Circadian Clock in Hypoxia through Inhibition of mTOR

Desoxycorticosterone pivalate‐salt treatment leads to non‐dipping hypertension in Per1 knockout mice

Making Time: Conservation of Biological Clocks from Fungi to Animals

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