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Protocols

JTK_CYCLE specifications

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Unique identifier OMICS_13325
Name JTK_CYCLE
Alternative name Jonckheere-Terpstra-Kendall-CYCLE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes

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  • person_outline Karl Kornacker

Publication for Jonckheere-Terpstra-Kendall-CYCLE

JTK_CYCLE citations

 (85)
library_books

Setting the pace: host rhythmic behaviour and gene expression patterns in the facultatively symbiotic cnidarian Aiptasia are determined largely by Symbiodinium

2018
Microbiome
PMCID: 5941691
PMID: 29739445
DOI: 10.1186/s40168-018-0465-9

[…] 64 were represented in the published protein database for this organism (which contains 29,269 predictions []). In order to detect rhythmic expression patterns, the 35,492 contigs were analysed using JTK_Cycle (v2.1) [–]. The rhythmic analysis identified 8253 genes (~ 23% of the differentially expressed transcripts) that cycled with either 24- or 12-h periodicity (p < 0.05). We could distinguish f […]

call_split

A proteomics landscape of circadian clock in mouse liver

2018
Nat Commun
PMCID: 5908788
PMID: 29674717
DOI: 10.1038/s41467-018-03898-2
call_split See protocol

[…] To determine the subset of cycling TFs, proteins, and transcripts. We performed JTK_CYCLE test with period range: 20–28 h and the amplitude and phase as free parameters. A statistical cut-off of p < 0.1 was used to define the cycling proteome, and p < 0.05 was used to define the […]

library_books

Genome wide excision repair in Arabidopsis is coupled to transcription and reflects circadian gene expression patterns

2018
Nat Commun
PMCID: 5904149
PMID: 29666379
DOI: 10.1038/s41467-018-03922-5

[…] The oscillation queries of the genomic bins and genes were performed using Metacycle software with the rhythmic signal detection methods ARS (ARSER), JTK (JTK_CYCLE) and LS (Lomb-Scargle). For genomic bins, we used JTK and LS methods and applied 0.05 p-value cutoff. For genic TS and NTS oscillation detection, we applied the three methods and used strict […]

library_books

Multimodal Regulation of Circadian Glucocorticoid Rhythm by Central and Adrenal Clocks

2018
PMCID: 5915959
PMID: 29713692
DOI: 10.1210/js.2018-00021

[…] ∼4% to 7% of gene transcripts follow circadian oscillations in their expression [, ]. Comparison of these two studies, following re-evaluation by equivalent criteria using a nonparametric algorithm (JTK_CYCLE) to detect rhythmic components [], yielded ~240 common genes that exhibit statistically significant circadian expression in both studies [; see for the full list of common rhythmic genes]. […]

library_books

A Conserved Circadian Function for the Neurofibromatosis 1 Gene

2018
Cell Rep
PMCID: 5898822
PMID: 29590612
DOI: 10.1016/j.celrep.2018.03.014

[…] me point using ImageJ analysis software, and the results were plotted as line graphs. For statistical analyses of circadian parameters, the calcium data were subjected to Jonckheere-Terpstra-Kendall (JTK)_CYCLE and Lomb-Scargle (LS) analysis using the Meta-cycle R program as described (). […]

library_books

Tidal and diel orchestration of behaviour and gene expression in an intertidal mollusc

2018
Sci Rep
PMCID: 5861051
PMID: 29559663
DOI: 10.1038/s41598-018-23167-y

[…] Transcript expression rhythmicity was performed using JTK_Cycle [v2.1]. JTK_Cycle is a statistical non-parametric based algorithm designed to efficiently identify and characterize cycling variables in large data sets. We used the aforementioned transcrip […]


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JTK_CYCLE institution(s)
Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA; Department of Pharmacology, Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Division of Sensory Biophysics, The Ohio State University, Columbus, OH, USA
JTK_CYCLE funding source(s)
This work was supported by the National Institute of Mental Health P50 Conte Center grant, the National Heart, Lung, and Blood Institute (NHBLI, 1R01HL097800), and Pennsylvania Commonwealth Health Research Formula Funds.

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