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Citations per year

Number of citations per year for the bioinformatics software tool ARSER
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This map represents all the scientific publications referring to ARSER per scientific context
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Protocols

ARSER specifications

Information


Unique identifier OMICS_13327
Name ARSER
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Microarray data file with a header line which records the time-points. The 1st column is probesets, other columns are expression values over time. It is assumed that the samples are linearly spaced (e.g., one point every 4 hrs, etc).
Output data Analytical results
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python, R
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
Scipy, Numpy, Matplotlib, Rpy2
Maintained Yes

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Maintainer


  • person_outline Zhen Su

Publication for ARSER

ARSER citations

 (17)
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 an […]

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Diel pattern of circadian clock and storage protein gene expression in leaves and during seed filling in cowpea (Vigna unguiculata)

2018
BMC Plant Biol
PMCID: 5813328
PMID: 29444635
DOI: 10.1186/s12870-018-1244-2
call_split See protocol

[…] e determination of existence of a circadian biological rhythm represented in the transcriptome data [] using the R package “MetaCycle” that provides functions and methods (JTK_CYCLE, Lomb-Scargle and ARSER) for detecting rhythmic signals from time series datasets (https://cran.r-project.org/web/packages/MetaCycle/index.html). JTK_CYCLE results include the P value (Pval, significative if P < 0.05), […]

library_books

Temporal Control of Metabolic Amplitude by Nocturnin

2018
Cell Rep
PMCID: 5815321
PMID: 29386110
DOI: 10.1016/j.celrep.2018.01.011

[…] ificant diurnal rhythmicity, similar to previous reports that examined circadian gene expression in WT mice (). Predictively, more stringent q values reduced the number of cycling genes with both the ARSER (ARS) and the Jonckheere-Terpstra-Kendall (JTK) algorithms (; ). However, although similar in number, only about half the cycling transcripts from each genotype were identified in both WT and KO […]

library_books

Episode like pulse testosterone supplementation induces tumor senescence and growth arrest down modulating androgen receptor through modulation of p ERK1/2, pARser81 and CDK1 signaling: biological implications for men treated with testosterone replacement therapy

2017
Oncotarget
PMCID: 5768363
PMID: 29371946
DOI: 10.18632/oncotarget.22776

[…] n extracts from LNCaP and CW22Rv1 treated with pulsed or continuous T concentrations. We found that both LNCaP and CW22rv1 cells exposed to pulsed T treatment (Figure ) showed a marked reduction of p-ARser81 levels, while only continuous treatment with high T (17.2 nM) concentration was able to reduce p-ARser81 levels in CW22rv1 cells. Accordingly, when we evaluated the levels of cyclin-dependent […]

library_books

Guidelines for Genome Scale Analysis of Biological Rhythms

2017
J Biol Rhythms
PMCID: 5692188
PMID: 29098954
DOI: 10.1177/0748730417728663

[…] re are numerous high-quality statistical approaches for detecting rhythmicity and estimating rhythmic parameters in large data sets. These include but are not limited to Haystack (), Lomb-Scargle (), ARSER (), CircWaveBatch (), JTK_Cycle (), and its successors, RAIN (), eJTK (), and ABSR (). Each has different strengths and weaknesses. To briefly summarize these methods, tests based on curve fitti […]

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Remodeling of the cycling transcriptome of the oyster Crassostrea gigas by the harmful algae Alexandrium minutum

2017
Sci Rep
PMCID: 5471176
PMID: 28615697
DOI: 10.1038/s41598-017-03797-4
call_split See protocol

[…] Sequencing outputs and bioinformatics treatments were carefully analyzed and checked several times to ensure the reliability of data supporting the discussion. Cycling transcripts were detected using ARSER with MetaCycle (version 1.1.0 on R (32-bit, version 3.2.2)). ARSER algorithm was developed and applied to high-throughput time-series analysis and particularly adapted to experimental designs wi […]


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ARSER institution(s)
Division of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
ARSER funding source(s)
This work was supported by the Ministry of Science and Technology of China (2008AA02Z312, 2006CB100105).

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