Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

TuxNet: A simple interface to process RNA sequencing data and infer gene regulatory networks

ABSTRACT: We obtained the transcriptional profiles from Arabidopsis WT and hb13 mutant roots

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE112563 | GEO | 2019/12/06

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

TuxNet: A simple interface to process RNA sequencing data and infer gene regulatory networks [XVE:PAN]

Project description:We obtained transcriptional profiles of roots from an XVE:PAN transgenic line under the control of the β-estradiol-inducible promoter, at times 0, 6, and 24 hours after induction of PAN expression.

2019-12-06 | GSE112564 | GEO

TuxNet: A simple interface to process RNA sequencing data and infer gene regulatory networks

Project description:TuxNet: A simple interface to process RNA sequencing data and infer gene regulatory networks

| PRJNA448186 | ENA

Identification of CLF-regulated transcripts using strand-specific RNA-sequencing in Arabidopsis

Project description:CURLY LEAF (CLF), the major histone methyltransferase of Polycomb Repressive Complex 2 (PRC2), modifies trimethylation of histone H3 lysine 27 (H3K27me3) and mediates dynamical chromatin repression in Arabidopsis. Here we used strand specific RNA-sequencing to profile Arabidopsis transcriptomes obtained from roots, shoots, flowers and siliques of Col-0 and clf-28 plants. Our analysis identified a large number of CLF-regulatedd transcripts in Arabidopsis. Transcriptome profiling in roots, shoots, inflorescences and siliques of WT and clf-28 plants with 3 biological replicates.

2016-03-28 | E-GEOD-61545 | biostudies-arrayexpress

TuxNet: A simple interface to process RNA sequencing data and infer gene regulatory networks [XVE:PAN]

Project description:TuxNet: A simple interface to process RNA sequencing data and infer gene regulatory networks [XVE:PAN]

| PRJNA448187 | ENA

HIRA regulate Arabidopsis dedifferentiation process

Project description:Plant development is characterised by the capacity to reprogram differentiated cells to initiate asexual reproduction and to produce new organs such as lateral roots. To test whether HIRA could be involved in aspects of developmental reprogramming we studied the effect of HIRA during de-differentiation Arabidopsis root tissue was digested with enzyme to generate protoplast. This process would induce plant cell dedifferentiation. Experiments were performed in WT and hira background to understand how hira affect plant dedifferentiation process.

2014-10-01 | E-GEOD-57044 | biostudies-arrayexpress

Symbiont-host interactome mapping reveals effector-targeted modulation of hormone networks and activation of host benefits

Project description:To identify candidate secreted proteins by the plant symbiont Serendipita indica, we infected the roots of the model plant Arabidopsis thaliana with fungal spores. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 conditions (mock and treated) and 2 timepoints (3 and 10 days after infection).

2023-06-07 | GSE222356 | GEO

Identification of CLF-regulated transcripts using strand-specific RNA-sequencing in Arabidopsis

2016-03-28 | GSE61545 | GEO

Gene duplication of type-B ARR transcription factors systematically extends transcriptional regulatory structures in Arabidopsis

Project description:Many of duplicated genes are enriched in signaling pathways. Recently, gene duplication of kinases has been shown to provide genetic buffering and functional diversification in cellular signaling. Transcription factors (TFs) are also often duplicated. However, how duplication of TFs affects their regulatory structures and functions of target genes has not been explored at the systems level. Here, we examined regulatory and functional roles of duplication of three major ARR TFs (ARR1, 10, and 12) in Arabidopsis cytokinin signaling using wild-type and single, double, and triple deletion mutants of the TFs. Comparative analysis of gene expression profiles obtained from Arabidopsis roots in wild-type and these mutants showed that duplication of ARR TFs systematically extended their transcriptional regulatory structures, leading to enhanced robustness and diversification in functions of target genes, as well as in regulation of cellular networks of target genes. Therefore, our results suggest that duplication of TFs contributes to robustness and diversification in functions of target genes by extending transcriptional regulatory structures. Duplication of TFs can confer an extension of transcriptional regulatory structures for target genes by providing new regulatory relationships between duplicated TFs and new or old target genes. To examine the nature of the extension in the regulatory structure, we performed gene expression profiling of Arabidopsis root tissues obtained from wild-type (WT) and deletion mutants of three type-B ARR1, 10, and 12. To examine how the extended regulatory structures by the duplicated ARR TFs are utilized for the responses to external CK, we generated gene expression profiles of WT Arabidopsis roots treated with mock or exogenous CK for 1 hour. Total RNAs were isolated from two biological replicates at each condition and used to measure gene expression level.

2015-02-03 | E-GEOD-62597 | biostudies-arrayexpress

A simple contagion process describes spreading of traffic jams in urban networks.

Project description:The spread of traffic jams in urban networks has long been viewed as a complex spatio-temporal phenomenon that often requires computationally intensive microscopic models for analysis purposes. In this study, we present a framework to describe the dynamics of congestion propagation and dissipation of traffic in cities using a simple contagion process, inspired by those used to model infectious disease spread in a population. We introduce two macroscopic characteristics for network traffic dynamics, namely congestion propagation rate β and congestion dissipation rate μ. We describe the dynamics of congestion spread using these new parameters embedded within a system of ordinary differential equations, similar to the well-known susceptible-infected-recovered (SIR) model. The proposed contagion-based dynamics are verified through an empirical multi-city analysis, and can be used to monitor, predict and control the fraction of congested links in the network over time.

| S-EPMC7138808 | biostudies-literature

kn09_vs_WT

Project description:Series of 6 repetitions of hybridization of treatment (kn09) and control (WT) each. Comparison of the proline-hypersensitive Arabidopsis kn09 mutant blocked in mitochondrial proline catabolism (roots treated with MS+100mM Glc for 48 h) versus WT (roots treated with MS+100mM Glc for 48 h). K. Deuschle et al., Plant J 27 (2001), pp. 345-356 Keywords: repeat sample

2005-01-01 | GSE1189 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data