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Comparison of expression profiles of WT and Nrf2AY/AY mutant macrophages under electrophilic stress agent

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE75177 | GEO | 2016/01/04

SECONDARY ACCESSION(S): PRJNA302712

REPOSITORIES: GEO

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Comparison of expression profiles of WT and Nrf2AY/AY mutant macrophages under electrophilic stress agent

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-01-04 | E-GEOD-75177 | biostudies-arrayexpress

Comparison of expression profiles of WT and Nrf2AY/AY mutant macrophages under electrophilic stress agent [ChIP-Seq]

Project description:Nrf2(A502Y) mutant macrophages Nrf2(AY/AY) macrophages were more susceptible to toxicity of xenobiotics. To confirm preferences of binding sequences of Nrf2 and Nrf2A502Y in vivo, we performed ChIP-Seq analyses using an anti-Nrf2 antibody on the DEM-treated peritoneal macrophages derived from Nrf2+/+ and Nrf2AY/AY mice.

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Comparison of expression profiles of WT and Nrf2AY/AY mutant macrophages under electrophilic stress agent [RNA-Seq]

Project description:Nrf2(A502Y) mutant failed to recognize cis-element required for induction of Nrf2 target genes.To examine whether Nrf2(A502Y) supports expression of a distinct gene set from that supported by Nrf2, RNA-Seq analysis was performed. We compared gene expression profiles in peritoneal macrophages from Nrf2+/+ and Nrf2AY/AY mice between basal and DEM (which is an electorophilic stress agent promoting Nrf2 induction)-treated conditions.

2016-01-04 | GSE75176 | GEO

Comparison of expression profiles of WT and Nrf2AY/AY mutant macrophages under electrophilic stress agent [ChIP-Seq]

2016-01-04 | E-GEOD-75175 | biostudies-arrayexpress

Comparison of expression profiles of WT and Nrf2AY/AY mutant macrophages under electrophilic stress agent [RNA-Seq]

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Comparison of expression profiles of WT and Nrf2AY/AY mutant macrophages under electrophilic stress agent

Project description:Comparison of expression profiles of WT and Nrf2AY/AY mutant macrophages under electrophilic stress agent

| PRJNA302712 | ENA

Oxidative and electrophilic stress conditions and the sor1 mutant

Project description:This SuperSeries is composed of the SubSeries listed below.

2011-07-15 | GSE30648 | GEO

Oxidative and electrophilic stress conditions and the sor1 mutant

Project description:This SuperSeries is composed of the following subset Series: GSE30645: Expression analysis of the singlet oxygen resistant 1 (sor1) mutant GSE30646: Response of Chlamydomonas reinhardtii to different oxidative and electrophilic stress conditions Refer to individual Series

2011-07-14 | E-GEOD-30648 | biostudies-arrayexpress

Comparison of Leaf Sheath Transcriptome Profiles with Physiological Traits of Bread Wheat Cultivars under Salinity Stress.

Project description:Salinity stress has significant negative effects on plant biomass production and crop yield. Salinity tolerance is controlled by complex systems of gene expression and ion transport. The relationship between specific features of mild salinity stress adaptation and gene expression was analyzed using four commercial varieties of bread wheat (Triticum aestivum) that have different levels of salinity tolerance. The high-throughput phenotyping system in The Plant Accelerator at the Australian Plant Phenomics Facility revealed variation in shoot relative growth rate and salinity tolerance among the four cultivars. Comparative analysis of gene expression in the leaf sheaths identified genes whose functions are potentially linked to shoot biomass development and salinity tolerance. Early responses to mild salinity stress through changes in gene expression have an influence on the acquisition of stress tolerance and improvement in biomass accumulation during the early "osmotic" phase of salinity stress. In addition, results revealed transcript profiles for the wheat cultivars that were different from those of usual stress-inducible genes, but were related to those of plant growth. These findings suggest that, in the process of breeding, selection of specific traits with various salinity stress-inducible genes in commercial bread wheat has led to adaptation to mild salinity conditions.

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A comparison of genomic profiles of complex diseases under different models.

Project description:BackgroundVarious approaches are being used to predict individual risk to polygenic diseases from data provided by genome-wide association studies. As there are substantial differences between the diseases investigated, the data sets used and the way they are tested, it is difficult to assess which models are more suitable for this task.ResultsWe compared different approaches for seven complex diseases provided by the Wellcome Trust Case Control Consortium (WTCCC) under a within-study validation approach. Risk models were inferred using a variety of learning machines and assumptions about the underlying genetic model, including a haplotype-based approach with different haplotype lengths and different thresholds in association levels to choose loci as part of the predictive model. In accordance with previous work, our results generally showed low accuracy considering disease heritability and population prevalence. However, the boosting algorithm returned a predictive area under the ROC curve (AUC) of 0.8805 for Type 1 diabetes (T1D) and 0.8087 for rheumatoid arthritis, both clearly over the AUC obtained by other approaches and over 0.75, which is the minimum required for a disease to be successfully tested on a sample at risk, which means that boosting is a promising approach. Its good performance seems to be related to its robustness to redundant data, as in the case of genome-wide data sets due to linkage disequilibrium.ConclusionsIn view of our results, the boosting approach may be suitable for modeling individual predisposition to Type 1 diabetes and rheumatoid arthritis based on genome-wide data and should be considered for more in-depth research.

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