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MetabolomicsConserved leaf–root metabolomic network asymmetry underpins divergent drought strategies
Plants orchestrate tissue-specific metabolic responses to osmotic stress, a major determinant of drought tolerance and crop productivity. Yet how leaf and root responses are coordinated to confer tolerance remains poorly understood. Here we show that drought tolerance in wheat is associated with a r...
2026-07-22 | MTBLS15125 | MetaboLights
MetabolomicsMetabolic reaction network-based recursive metabolite annotation for untargeted metabolomics (Aging fruit fly negative mode)

Large-scale metabolite annotation is a challenge in liquid chromatogram-mass spectrometry (LC-MS)-based untargeted metabolomics. Here, we develop a metabolic reaction network (MRN)-based recursive algorithm (MetDNA) that expands metabolite annotations without the need for a comprehensive standard...

2019-03-26 | MTBLS615 | MetaboLights
TranscriptomicsA mesodermal gene regulatory network directed by zebrafish No tail
Using chromatin immunoprecipitation combined with microarrays we have identified targets of No tail (Ntl), a zebrafish Brachyury ortholog that plays a central role in mesoderm formation. We show that Ntl regulates a downstream network of other transcription factors and identify an in vivo Ntl bindin...
ORGANISM(S): Danio rerio 
2009-02-19 | E-GEOD-12331 | biostudies-arrayexpress
TranscriptomicsNetwork Biology of Tumor Stem-like Cells Identified a Regulatory Role of CBX5 in Lung Cancer
Mounting evidence points to a link between a cancer possessing stem-like properties and a worse prognosis. To understand the biology, a common approach is to integrate network biology with signal processing mechanics. That said, even with the right tools, predicting the risk for a highly susceptible...
ORGANISM(S): Homo sapiens 
2012-08-17 | E-GEOD-35603 | biostudies-arrayexpress
ProteomicsSpecificity and dynamics of H2O2 detoxification by the cytosolic redox regulatory network as revealed by in vitro reconstitution
The thiol redox state is a decisive functional characteristic of proteins in cell biology. Plasmatic cell compartments maintain a thiol-based redox regulatory network linked to the glutathione/glutathione disulfide couple (GSH/GSSG) and the NAD(P)H system. The basic network constituents are known an...
ORGANISM(S): Escherichia Coli 
2025-01-21 | PXD048374 | JPOST Repository
TranscriptomicsInferring the stress-activated signaling network in yeast through multi-omic data integration
Transcriptome profiling of yeast mutant strains responding to 0.7M NaCl treatment for 30 minutes. This study identified affected genes in each mutant and used it to computationally infer the complete NaCl-activated signaling network in yeast. Two-color fluorescence arrays reporting on mRNA abundanc...
ORGANISM(S): Saccharomyces cerevisiae 
2014-12-03 | E-GEOD-51844 | biostudies-arrayexpress
TranscriptomicsModeling regulatory relationships in Arabidopsis immune signaling network.
Expression profiles of 22 reference Arabidopsis immunity mutants were collected using the Arabidopsis Pathoarray 464_001 (GPL3638) in order to build a network model predicting the Arabidopsis immune signaling network. Biological signaling processes may be mediated by complex networks in which netwo...
ORGANISM(S): Arabidopsis thaliana 
2010-07-22 | E-GEOD-19663 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of human 48 clinical breast cancer arrays to perform statistical identification of gene association by CID in application of constructing ER regulatory network
A variety of high-throughput techniques are now available for constructing comprehensive gene regulatory networks in systems biology. In this study, we report a new statistical approach for facilitating in silico inference of regulatory network structure. The new measure of association, coefficient ...
ORGANISM(S): Homo sapiens 
2009-07-19 | E-GEOD-17041 | biostudies-arrayexpress
TranscriptomicsSystems biology of interstitial lung diseases
This SuperSeries is composed of the following subset Series: GSE21369: Gene expression profiles of interstitial lung disease (ILD) patients GSE21394: MicroRNA expression profiles of interstitial lung disease (ILD) patients Refer to individual Series
ORGANISM(S): Homo sapiens 
2011-04-19 | E-GEOD-21411 | biostudies-arrayexpress
TranscriptomicsStructural systems biology evaluation of metabolic thermotolerance in Escherichia coli
Investigation of whole genome gene expression level in E. coli K-12 MG1655 in glucose M9 minimal media with/without heatshock A six chip study using total RNA recovered from E. coli K-12 MG1655 grown up to OD600nm 0.6 (mid-exponential phase) in M9 minimal media supplemented with 0.2% glucose with/wi...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2013-06-20 | E-GEOD-42675 | biostudies-arrayexpress
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