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MetabolomicsMulti-omics and biophysical phosphoproteomics uncover functional phosphorylation networks of BRAFV600E-driven signaling

Dysregulated kinase activity drives oncogenic signalling, perturbs cellular homeostasis, and promotes tumour progression. Despite major success in targeting kinases therapeutically, the downstream consequences of kinase inhibition and the mechanisms underlying drug resistance remain incompletely ...

2025-12-09 | MTBLS7390 | MetaboLights
MetabolomicsDifferential expression of Transcriptomics and Metabolomics in different developmental periods of poria cocos

Poria cocos, a traditional medicinal fungus, exhibits a wide array of biological activities. Through the integration of metabolomic and transcriptomic analyses, we have determined that the development of Poria cocos mycelia is predominantly propelled by biochemical reactions triggered by oxidativ...

2025-03-26 | MTBLS11738 | MetaboLights
MetabolomicsSimilar, but different: structurally related azelaic acid and hexanoic acid trigger differential metabolomic and transcriptomic responses in tobacco cells
BACKGROUND: Plants respond to various stress stimuli by activating an enhanced broad-spectrum defensive ability. The development of novel resistance inducers represents an attractive, alternative crop protection strategy. In this regard, hexanoic acid (Hxa, a chemical elicitor) and azelaic acid (Aza...
2018-10-17 | MTBLS559 | MetaboLights
ProteomicsEffect of Phosphorylation on the Collision Cross Sections of Peptide Ions in Ion Mobility Spectrometry
The insertion of ion mobility spectrometry (IMS) between LC and MS can improve peptide identification in both proteomics and phosphoproteomics by providing structural information that is complementary to LC and MS, because IMS separates ions on the basis of differences in their shapes and charge sta...
ORGANISM(S): Homo Sapiens (human) 
2021-01-14 | PXD019746 | JPOST Repository
TranscriptomicsCTD tyrosine phosphorylation impairs termination factor recruitment to transcribing RNA polymerase II
ChIP-chip was performed to identify the genomic binding locations for the termination factors Nrd1, and Rtt103, and for RNA polymerase (Pol) II phosphorylated at the tyrosine 1 and threonine 4 position of its C-terminal domain (CTD). In different phases of the transcription cycle, Pol II recruits di...
ORGANISM(S): Saccharomyces cerevisiae 
2012-06-29 | E-MTAB-1060 | biostudies-arrayexpress
TranscriptomicsR-loops are marks for histone H3 Ser10 phosphorylation and chromatin compaction
R-loops are transcription by-products that may constitute a threat to genome integrity. In addition to specific enzymes to remove them, eukaryotes rely on a number of mRNP biogenesis factors such as the THO complex, to prevent co-transcriptional R-loop formation. We show in Saccharomyces cerevisiae ...
ORGANISM(S): Saccharomyces cerevisiae 
2013-11-13 | E-GEOD-46627 | biostudies-arrayexpress
ProteomicsProteomic profiling of human monocytes stimulated in vitro with N. meningitidis
Meningococcal sepsis is an overwhelming form of the sepsis syndrome which may cause mortality within 12-24 hours in previously healthy children and adults, where the causative infectious agent is N. meningitidis, an obligate human pathogen. The genomic changes induced by N. meningitidis are modulate...
ORGANISM(S): Homo sapiens 
2017-12-15 | E-MTAB-4795 | biostudies-arrayexpress
ProteomicsAgonist-selective NOP receptor phosphorylation correlates in vitro and in vivo and reveals differential post-activation signaling by chemically diverse agonists
Agonists for the nociceptin/orphanin FQ opioid peptide NOP receptor, a member of the opioid receptor family, are under active investigation as novel analgesics, but their modes of signaling are less well characterized than those for other members of the opioid receptor family. Therefore, we investig...
ORGANISM(S): Mus musculus (Mouse) 
2020-05-26 | PXD012908 | Pride
Brain Opioid receptor family Mouse Biological Pharmacology Post-translational modification Nanolc-ms/ms cid/etd Phosphorylation 
ProteomicsIdentification of differential phosphoproteins reveled complex responses of soybean to phosphate starvation through reversible protein phosphorylation
Phosphorus (P) deficiency is considered as a major constraint on crop production. Although a set of adaptative strategies are extensively suggested in soybean (Glycine max) to phosphate(Pi) deprivation, molecular mechanisms underlying reversible protein phosphorylation in soybean responses to P defi...
ORGANISM(S): Glycine max 
2021-06-13 | PXD025771 | Pride
Soybean roots Phosphorylation Phosphate starvation Differential phosphoproteins 
TranscriptomicsGenome-wide activity-dependent MeCP2 phosphorylation regulates nervous system development and function [cultured cortical neurons]
To examine potential differences in activity-dependent gene expression, we analyzed mRNA expression in cultured neurons isolated from Wild-type vs MeCP2 S421A mice at 0 (unstimulated), 1 or 6 hours after membrane depolarization by exposure to high extracellular KCl (55mM) All mice were male litterma...
ORGANISM(S): Mus musculus 
2011-09-07 | E-GEOD-31849 | biostudies-arrayexpress
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