Abstract：
Background:Progress in high-throughput molecular methods accompanied by more complex experimental designs demands novel data visualisation solutions. To specifically answer the question which parts of the specifical biological system are responding in particular perturbation, integrative approach in which experimental data are superimposed on a prior knowledge network is shown to be advantageous. Results:We have developed DiNAR, Differential Network Analysis in R, a user-friendly application with dynamic visualisation that integrates multiple condition high-throughput data and extensive biological prior knowledge. Implemented differential network approach and embedded network analysis allow users to analyse condition-specific responses in the context of topology of interest (e.g. immune signalling network) and extract knowledge concerning patterns of signalling dynamics (i.e. rewiring in network structure between two or more biological conditions). We validated the usability of software on the Arabidopsis thaliana and Solanum tuberosum datasets, but it is set to handle any biological instances. Conclusions:DiNAR facilitates detection of network-rewiring events, gene prioritisation for future experimental design and allows capturing dynamics of complex biological system. The fully cross-platform Shiny App is hosted and freely available at https://nib-si.shinyapps.io/DiNAR. The most recent version of the source code is available at https://github.com/NIB-SI/DiNAR/ with a DOI 10.5281/zenodo.1230523 of the archived version in Zenodo.
journal_name
Plant Methodsjournal_title
Plant methodsauthors
Zagorščak M,Blejec A,Ramšak Ž,Petek M,Stare T,Gruden Kdoi
10.1186/s13007-018-0345-0subject
Has Abstractpub_date
2018-08-30 00:00:00pages
78issn
1746-4811pii
345journal_volume
14pub_type
杂志文章相关文献
Plant Methods文献大全abstract：:Receptor-like protein kinases (RLKs) are a large and important group of plant proteins involved in numerous aspects of development and stress response. Within this family, homo-oligermization of receptors followed by autophosphorylation of the intracellular protein kinase domain appears to be a widespread mechanism to...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-9-22
更新日期：2013-06-26 00:00:00
abstract：Background:Chickpea (Cicer arietinum L.), an important legume crop is one of the major source of dietary protein. Developing an efficient and reproducible transformation method is imperative to expedite functional genomics studies in this crop. Here, we present an optimized and detailed procedure for Agrobacterium rhiz...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-018-0315-6
更新日期：2018-07-06 00:00:00
abstract：Background:Deep rooting is one of the most promising plant traits for improving crop yield under water-limited conditions. Most root phenotyping methods are designed for laboratory-grown plants, typically measuring very young plants not grown in soil and not allowing full development of the root system. Results:This s...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-019-0533-6
更新日期：2019-12-09 00:00:00
abstract：: Generating and identifying transformants is essential for many studies of gene function. In Arabidopsis thaliana, a revolutionary protocol termed floral dip is now the most widely used transformation method. Although robust, it involves a number of relatively time-consuming and laborious steps, including manipulating...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-5-3
更新日期：2009-02-27 00:00:00
abstract：: Large-scale genetic screens in Arabidopsis are a powerful approach for molecular dissection of complex signaling networks. However, map-based cloning can be time-consuming or even hampered due to low chromosomal recombination. Current strategies using next generation sequencing for molecular identification of mutatio...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-8-12
更新日期：2012-03-30 00:00:00
abstract：Background:Low pollen viability may limit grapevine yield under certain conditions, causing relevant economic losses to grape-growers. It is usually evaluated by the quantification of the number of viable and non-viable pollen grains that are present in a sample after an adequate pollen grain staining procedure. Althou...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-017-0267-2
更新日期：2018-01-09 00:00:00
abstract：Background:Monitoring the timing of seedling emergence and early development via high-throughput phenotyping with computer vision is a challenging topic of high interest in plant science. While most studies focus on the measurements of leaf area index or detection of specific events such as emergence, little attention ...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-020-00647-9
更新日期：2020-07-30 00:00:00
abstract：:[This corrects the article DOI: 10.1186/s13007-019-0478-9.]. ...
journal_title：Plant methods
pub_type： 已发布勘误
doi：10.1186/s13007-019-0495-8
更新日期：2019-10-10 00:00:00
abstract：Background:Nowadays, there is an increasing demand for fast and reliable plant biomolecular analyses. Conventional methods for the isolation of nucleic acids are time-consuming and require multiple and often non-automatable steps to remove cellular interferences, with consequence that sample preparation is the major bo...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-019-0408-x
更新日期：2019-03-09 00:00:00
abstract：Background:The demand for effective use of water resources has increased because of ongoing global climate transformations in the agriculture science sector. Cost-effective and timely distributions of the appropriate amount of water are vital not only to maintain a healthy status of plants leaves but to drive the produ...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-019-0522-9
更新日期：2019-11-18 00:00:00
abstract：BACKGROUND:In the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. Databases provide crucial solutions: they store, organize and allow information to be queried, they enhance the visibility of newly produced data by comparing them with previously published r...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-7-8
更新日期：2011-03-29 00:00:00
abstract：BACKGROUND:Genetic studies on the molecular mechanisms of the regulation of root growth require the characterisation of a specific root phenotype to be linked with a certain genotype. Such studies using classical labour-intensive methods are severely hindered due to the technical limitations that are associated with th...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-016-0135-5
更新日期：2016-06-24 00:00:00
abstract：:Modern agriculture has created a demand for plant biotechnology products that provide durable resistance to insect pests, tolerance of herbicide applications for weed control, and agronomic traits tailored for specific geographies. These transgenic trait products require a modular and sequential multigene stacking pla...
journal_title：Plant methods
pub_type： 杂志文章,评审
doi：10.1186/s13007-016-0111-0
更新日期：2016-02-01 00:00:00
abstract：Background:The stomata of plants mainly regulate gas exchange and water dispersion between the interior and external environments of plants and play a major role in the plants' health. The existing methods of stomata segmentation and measurement are mostly for specialized plants. The purpose of this research is to deve...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-019-0453-5
更新日期：2019-07-03 00:00:00
abstract：Background:In-field measurement of yield and growth rate in pasture species is imprecise and costly, limiting scientific and commercial application. Our study proposed a LiDAR-based mobile platform for non-invasive vegetative biomass and growth rate estimation in perennial ryegrass (Lolium perenne L.). This included de...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-019-0456-2
更新日期：2019-07-10 00:00:00
abstract：BACKGROUND:The inability to genetically transform any fern species has been a major technical barrier to unlocking fern biology. Initial attempts to overcome this limitation were based on transient transformation approaches or achieved very low efficiencies. A highly efficient method of stable transformation was recent...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-015-0080-8
更新日期：2015-07-03 00:00:00
abstract：BACKGROUND:Transcription factors (TFs) coordinate precise gene expression patterns that give rise to distinct phenotypic outputs. The identification of genes and transcriptional networks regulated by a TF often requires stable transformation and expression changes in plant cells. However, the production of stable trans...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-016-0141-7
更新日期：2016-10-19 00:00:00
abstract：BACKGROUND:Fluorescent proteins are extraordinary tools for biology studies due to their versatility; they are used extensively to improve comprehension of plant-microbe interactions. The viral infection process can easily be tracked and imaged in a plant with fluorescent protein-tagged viruses. In plants, fluorescent ...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-10-22
更新日期：2014-07-05 00:00:00
abstract：BACKGROUND:There is considerable interest in rapid assays or screening systems for assigning gene function. However, analysis of gene function in the flowers of some species is restricted due to the difficulty of producing stably transformed transgenic plants. As a result, experimental approaches based on transient gen...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-3-1
更新日期：2007-01-08 00:00:00
abstract：BACKGROUND:The main aim of this study was to improve fungal resistance in bread wheat via transgenesis. Transgenic wheat plants harboring barley chitinase (chi26) gene, driven by maize ubi promoter, were obtained using biolistic bombardment, whereas the herbicide resistance gene, bar, driven by the CaMV 35S promoter wa...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-017-0191-5
更新日期：2017-05-22 00:00:00
abstract：BACKGROUND:Artificial chromosomes (ACs) are a promising next-generation vector for genetic engineering. The most common methods for developing AC constructs are to clone and combine centromeric DNA and telomeric DNA fragments into a single large DNA construct. The AC constructs developed from such methods will contain ...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-7-10
更新日期：2011-04-15 00:00:00
abstract：BACKGROUND:Maize haploid breeding technology can be used to rapidly develop homozygous lines, significantly shorten the breeding cycle and improve breeding efficiency. Rapid and accurate sorting haploid kernels is a prerequisite for the large-scale application of this technology. At present, the automatic haploid sorti...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-020-00703-4
更新日期：2021-01-06 00:00:00
abstract：:Plants are good sources of biologically active compounds with antimicrobial activity, including polypeptides. Antimicrobial peptides (AMPs) represent one of the main barriers of plant innate immunity to environmental stress factors and are attracting much research interest. There are some extraction methods for isolat...
journal_title：Plant methods
pub_type： 杂志文章,评审
doi：10.1186/s13007-020-00687-1
更新日期：2020-10-23 00:00:00
abstract：BACKGROUND:Transient gene expression systems are indispensable tools in molecular biology. Yet, their routine application is limited to few plant species often requiring substantial equipment and facilities. High chloroplast and chlorophyll content may further impede downstream applications of transformed cells from gr...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-8-14
更新日期：2012-05-04 00:00:00
abstract：Background:High throughput non-destructive phenotyping is emerging as a significant approach for phenotyping germplasm and breeding populations for the identification of superior donors, elite lines, and QTLs. Detection and counting of spikes, the grain bearing organs of wheat, is critical for phenomics of a large set ...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-020-00582-9
更新日期：2020-03-18 00:00:00
abstract：BACKGROUND:We previously developed a high-throughput system called 'Ice-Cap' for growing Arabidopsis seedlings in a 96-well format and rapidly collecting tissue for subsequent DNA extraction and genotyping. While the originally described Ice-Cap method is an effective tool for high-throughput genotyping, one shortcomin...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-3-8
更新日期：2007-06-12 00:00:00
abstract：: Microarrays are routine tools for transcript profiling, and genomic tiling arrays such as the Arabidopsis AGRONOMICS1 arrays have been found to be highly suitable for such experiments because changes in genome annotation can be easily integrated at the data analysis level. In a transcript profiling experiment, RNA la...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-8-18
更新日期：2012-06-13 00:00:00
abstract：: Research in plant molecular biology involves DNA purification on a daily basis. Although different commercial kits enable convenient extraction of high-quality DNA from E. coli cells, PCR and agarose gel samples as well as plant tissues, each kit is designed for a particular type of DNA extraction work, and the cost ...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-6-1
更新日期：2010-01-14 00:00:00
abstract：BACKGROUND:Allotetraploid white clover (Trifolium repens L.) is an important forage legume widely cultivated in most temperate regions. Only a small number of microsatellite markers are publicly available and can be utilized in white clover breeding programs. The objectives of this study were to develop an integrated a...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-4-19
更新日期：2008-07-16 00:00:00
abstract：BACKGROUND:In eukaryotic cells, the proteasome maintains homeostasis by selectively degrading regulatory and misfolded proteins, and in doing so contributes to the amino acid pool. Inhibition of the proteasome in yeast and human cells decreases de novo protein synthesis. However, it is not know if proteasome inhibition...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-016-0120-z
更新日期：2016-03-16 00:00:00
