npstat specifications


Unique identifier OMICS_05826
Name npstat
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for npstat

npstat in publications

PMCID: 5640784
PMID: 29062282
DOI: 10.3389/fphys.2017.00775

[…] separate dimerization step was neglected, because the oligomerization state of stat3 was not assessed by experiments. active, dimeric pstat3 subsequently translocates to the nuclear compartment, and npstat3 promotes transcription of socs3 and app genes. the generation of cytoplasmic rna was modeled including a delay (τ; macdonald, ; bachmann et al., ) for both socs3 and app genes to account […]

PMCID: 4975441
PMID: 27494133
DOI: 10.1371/journal.pcbi.1005049

[…] step of nuclear phosphorylated (np) stat5 was included to be able to distinguish dephosphorylation and nuclear export of stat5 []. (iii) the regulation of the socs3 promotor binding activity by npstat5 was described by a hill coefficient to allow non-linear transcriptional activity. in addition, the receptor phosphatase shp1 that is known to be restricted to hematopoietic cells […]

PMCID: 4604096
PMID: 26461136
DOI: 10.1371/journal.pone.0140462

[…] count of two reads. the nucleotide diversity and the genetic differentiation from the reference genome that are needed to set prior probabilities in the bayesian model of snape were calculated by npstat []. we used the bedtools software [] to calculate sequencing depth or depth of coverage per site, defined as the number of times each base was sequenced per individual or per population pool. […]

PMCID: 3980879
PMID: 24719192
DOI: 10.7554/eLife.01944.018

[…] differential equations for the other variablesare:dnpmhc(t)dt=−kantigenconsumption(∑i=1ncellntcr•pmhci(t))dnil2rαi(t)dt=kreceptordegradation·[ntcr>il2rα(max)·h(ntcr•pmhci(t),τreceptorproduction)+npstat5>il2rα(max)·ppstat5i(t)−nil2rα(t)]dnil2rβi(t)dt=kreceptordegradation·[nil2rβ(0)+(nil2rβ(max)−nil2rβ(0))·h(ntcr•pmhci(t),τreceptorproduction)]−kreceptordegradation·nil2rβi(t)dnil2•il2ri(t)dt= […]

PMCID: 3787051
PMID: 24098642
DOI: 10.1371/journal.pone.0074335

[…] the ode systems is composed out of the rate equations by, the volume factors pl and pl account for transitions between different compartments and are determined experimentally. the species npstat5, cisnrna1–5 and socs3nrna1–5 are located in the nuclear compartment, the remaining species in the cytoplasmatic compartment. the initial condition are set to zero except for, the parameter […]

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npstat institution(s)
Center for Research in Agricultural Genomics (CRAG), UAB, Bellaterra, Spain

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