Abstract:
:The abundance of RNA species and their response to perturbations are set by the kinetics rates of RNA synthesis, processing, and degradation. However, the visualization, interpretation, and manipulation of these data require familiarity with mathematical modeling and command line tools. INSPEcT-GUI is an R-Shiny interface that allows researchers without specific training to effortlessly explore how the fine kinetic regulation of the RNA life cycle can shape gene expression programs. In particular, it allows to: (i) interactively visualize gene-level RNA dynamics; (ii) refine the model fit of experimental data; (iii) test alternative regulatory models; (iv) explore, independently from the availability of data, how the combined action of the RNA kinetic rates impacts on premature and mature RNA. INSPEcT-GUI is freely available within the R/Bioconductor package INSPEcT at http://bioconductor.org/packages/INSPEcT/. An HTML vignette including documentation on the tool startup and usage, executable examples, and a video demonstration, are available at: http://bioconductor.org/packages/release/bioc/vignettes/INSPEcT/inst/doc/INSPEcT_GUI.html.
journal_name
Front Genetjournal_title
Frontiers in geneticsauthors
de Pretis S,Furlan M,Pelizzola Mdoi
10.3389/fgene.2020.00759subject
Has Abstractpub_date
2020-07-17 00:00:00pages
759issn
1664-8021journal_volume
11pub_type
杂志文章abstract::Circadian rhythms produce a biological measure of the time of day. In plants, circadian regulation forms an essential adaptation to the fluctuating environment. Most of our knowledge of the molecular aspects of circadian regulation in plants is derived from laboratory experiments that are performed under controlled co...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2019.01239
更新日期:2019-11-29 00:00:00
abstract:Objective:Extensive literature put forward the link between sleep and type 2 diabetes mellitus (T2DM), however, little is known about the underlying causality of the associations. Here we aim to assess the causal relationships between five major sleep-related traits and T2DM. Design Setting and Participants:Two-sample...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.607865
更新日期:2020-12-15 00:00:00
abstract::Pacu (Piaractus mesopotamicus) is a Neotropical fish of major importance for South American aquaculture. Septicemia caused by Aeromonas hydrophila bacteria is currently considered a substantial threat for pacu aquaculture that have provoked infectious disease outbreaks with high economic losses. The understanding of m...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00604
更新日期:2020-06-09 00:00:00
abstract::The genetic diversity of the sheep breeds in the Arab countries might be considered to be a mirror of the ecology of the region. In this study, the genetic structure and diversity of sheep breeds from Saudi Arabia (Harri, Najdi, Naemi, Arb, and Rufidi) and Awassi sheep from Jordan as an out-group were investigated usi...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00408
更新日期:2018-09-25 00:00:00
abstract::Recent studies have revealed that the RNA N6-methyladenosine (m6A) modification plays a critical role in a variety of biological processes and associated with multiple diseases including cancers. Till this day, transcriptome-wide m6A RNA methylation sites have been identified by high-throughput sequencing technique co...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00266
更新日期:2019-04-03 00:00:00
abstract::Pathway analysis is a powerful method for data analysis in genomics, most often applied to gene expression analysis. It is also promising for single-nucleotide polymorphism (SNP) data analysis, such as genome-wide association study data, because it allows the interpretation of variants with respect to the biological p...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2017.00174
更新日期:2017-11-07 00:00:00
abstract::During plant-pathogen interactions, pathogens secrete many rapidly evolving, small secreted proteins (SSPs) that can modify plant defense and permit pathogens to colonize plant tissue. The fungal pathogen Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB), one of the most important foliar diseas...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00469
更新日期:2020-05-12 00:00:00
abstract::Goats (Capra hircus) are an economically important livestock species providing meat and milk across the globe. They are of particular importance in tropical agri-systems contributing to sustainable agriculture, alleviation of poverty, social cohesion, and utilisation of marginal grazing. There are excellent genetic an...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01080
更新日期:2019-11-04 00:00:00
abstract::Pathogenic microorganism analysis based on next-generation sequencing technology is an important tool for clinical diagnosis, public health surveillance, and outbreak investigation. However, scientific researchers without the relevant background lack the time, training, or infrastructure to use large data sets or inst...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.01007
更新日期:2020-08-31 00:00:00
abstract::Recruitment of diverse populations and subjects living in Medically Underserved Areas and Populations (MUA/P's) into clinical trials is a considerable challenge. Likewise, representation of African-Americans in pharmacogenetic trials is often inadequate, but critical for identifying genetic variation within and betwee...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00571
更新日期:2020-06-25 00:00:00
abstract::In this study, we examined whether smoking and drinking affect sperm quality and the DNA methylation of the repetitive element LINE-1, MEST, P16, H19, and GNAS in sperm. Semen samples were obtained from 143 male residents in a minority-inhabited district of Guizhou province in southwest China. Quantitative DNA methyla...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01001
更新日期:2019-10-18 00:00:00
abstract::The Galápagos Islands are known to have experienced significant drought during the Quaternary. The loss of mesophytic upland habitats has been suggested to underlie the relatively lower endemism of upland compared with lowland plant assemblages. A fossil pollen record spanning the last 26,000 years from an upland bog ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2013.00269
更新日期:2013-12-03 00:00:00
abstract::The aging of the population represents one of the largest healthcare challenges facing the world today. The available scientific evidence shows that interventions are available now that can target fundamental "aging" processes or pathways. Sufficient economic evidence is available to argue convincingly that this appro...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2015.00171
更新日期:2015-07-14 00:00:00
abstract::The Apelin (APLN)/apelin receptor (APLNR) signaling pathway is a newly identified regulator in various cardiovascular diseases, which is considered as a candidate pathway for the occurrence of coronary heart disease (CHD), depression, and anxiety. The goal of this study was to investigate the association between APLN/...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00893
更新日期:2020-08-11 00:00:00
abstract::Telomeres are important for maintaining genomic stability. Telomere length has been associated with aging, disease, and mortality and is highly heritable (∼82%). In this study, we aimed to identify rare genetic variants associated with telomere length using whole-exome sequence data. We studied 1,303 participants of t...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00337
更新日期:2020-04-30 00:00:00
abstract::Gene expression profiling has been widely used to characterize cell status to reflect the health of the body, to diagnose genetic diseases, etc. In recent years, although the cost of genome-wide expression profiling is gradually decreasing, the cost of collecting expression profiles for thousands of genes is still ver...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01077
更新日期:2019-11-12 00:00:00
abstract::It is broadly expected that next generation sequencing will ultimately generate a complete genome as is the latest goat reference genome (ARS1), which is considered to be one of the most continuous assemblies in livestock. However, the rich diversity of worldwide goat breeds indicates that a genome from one individual...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01169
更新日期:2019-11-15 00:00:00
abstract::Human CYP3A enzymes (including CYP3A4 and CYP4A5) metabolize about 40% of all drugs and numerous other environmental and endogenous substances. CYP3A activity is highly variable within and between humans. As a consequence, therapy with standard doses often results in too low or too high blood and tissue concentrations...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00944
更新日期:2020-08-21 00:00:00
abstract::Recent advances in genomics and proteomics generated a large amount of trans regulatory data such as those mediated by RNA binding proteins (RBPs) and microRNAs. Since many trans regulators target 3' UTR of mRNA transcripts, it is likely that there would be interactions, i.e., competitive or cooperative effect, among ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.515094
更新日期:2020-09-08 00:00:00
abstract::MicroRNAs (miRNAs) are small RNAs repressing gene expression. They contribute to many physiological processes and pathologies. Consequently, strategies for manipulation of the miRNA pathway are of interest as they could provide tools for experimental or therapeutic interventions. One of such tools could be small chemi...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00045
更新日期:2018-02-27 00:00:00
abstract::Understanding the molecular basis of cell function and ultimate phenotypes is crucial for the development of biological markers. With this aim, several RNA-seq studies have been devoted to the characterization of the transcriptome of ejaculated spermatozoa in relation to sperm quality and fertility. Semen quality foll...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00299
更新日期:2019-04-16 00:00:00
abstract::Trauma is a leading cause of morbidity and mortality. It is unclear why some trauma victims follow a complicated clinical course and die, while others, with apparently similar injury characteristics, do not. Interpatient genomic differences, in the form of single nucleotide polymorphisms (SNPs), have been associated p...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01115
更新日期:2019-11-08 00:00:00
abstract::Predicting how species interactions evolve requires that we understand the mechanistic basis of coevolution, and thus the functional genotype-by-genotype interactions (G × G) that drive reciprocal natural selection. Theory on host-parasite coevolution provides testable hypotheses for empiricists, but depends upon mode...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2014.00077
更新日期:2014-04-11 00:00:00
abstract::Leukemia, specifically acute myeloid leukemia (AML), is a common malignancy that can be differentiated into multiple subtypes based on leukemogenic history and etiology. Although genetic aberrations, particularly cytogenetic abnormalities and mutations in known oncogenes, play an integral role in AML development, epig...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2019.00133
更新日期:2019-03-01 00:00:00
abstract:Objective:This study reports a Chinese patient with a Congenital Disorder of Glycosylation (CDG) caused by compound-heterozygous mutations in the Conserved Oligomeric Golgi 5 (COG5) gene and thereby offers concrete evidence for early diagnosis. Methods:The clinical manifestations, the results of laboratory examination...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00168
更新日期:2020-02-27 00:00:00
abstract::Nuclear factor Y (NF-Y) is a heterotrimeric transcription factor with the ability to bind to a CCAAT box in nearly all eukaryotes. However, the function of NF-Y in the life-history traits of insects is unclear. Here, we identified three NF-Y subunits, NlNF-YA, NlNF-YB, and NlNF-YC, in the wing-dimorphic brown planthop...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.585320
更新日期:2020-11-03 00:00:00
abstract::Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is the primary cause of Phomopsis seed decay (PSD) in soybean, Glycine max (L.) Merrill. This disease results in poor seed quality and is one of the most economically important seed diseases in soybean. The objectives of this study were to infer protein-prot...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00104
更新日期:2018-04-03 00:00:00
abstract::Proliferation and differentiation of preadipocyte are essential for the formation of fat tissues. However, the genes that regulate the early stage of preadipocyte differentiation in chicken have remained elusive. Here we identify a novel spliced variant of the DNA methyltransferase Dnmt3a gene, named Dnmt3a3, that con...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00115
更新日期:2020-02-25 00:00:00
abstract::Assortative mating is a universal feature of human societies, and individuals from ethnically diverse populations are known to mate assortatively based on similarities in genetic ancestry. However, little is currently known regarding the exact phenotypic cues, or their underlying genetic architecture, which inform anc...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00359
更新日期:2019-04-24 00:00:00
abstract::Cyprinids are the most important group of farmed fish globally in terms of production volume, with common carp (Cyprinus carpio) being one of the most valuable species of the group. The use of modern selective breeding methods in carp is at a formative stage, implying a large scope for genetic improvement of key produ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00082
更新日期:2018-03-13 00:00:00