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MetabolomicsAberrant accumulation of cyclin D1 rewires glutamine metabolism via loss of IDH3 generating metabolic vulnerability in ESCC and HNSCC

Excessive cyclin D1 accumulation is a frequent oncogenic event in head and neck squamous cell carcinoma (HNSCC) and esophageal squamous cell carcinoma (ESCC). Although classically associated with enhanced proliferation and genomic instability, we reveal that cyclin D1 dysregulation induces unexpe...

2026-08-24 | MTBLS13687 | MetaboLights
MetabolomicsDistinct microbes, metabolites, and the host genome define the multi-omics profiles in right-sided and left-sided colon cancer

BACKGROUND: Studies have reported clinical heterogeneity between right-sided colon cancer (RCC) and left-sided colon cancer (LCC). However, none of these studies used multi-omics analysis combining genetic regulation, microbiota and metabolites to explain the site-specific differ...

2024-12-16 | MTBLS10232 | MetaboLights
Proteomics3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes
Studying the dynamics of three-dimensional (3D) chromatin structure is essential to the understanding of biological processes in the nucleus. Integrative analysis of multi-omics data in recent publications have provided comprehensive and multilevel insight into 3D genome organization emphasizing its...
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
2024-07-30 | MSV000095480 | MassIVE
TranscriptomicsExpression data of two human cancer cell lines cultivated in 2-dimensional (2D) vs. 3-dimensional (3D) cell culture
3D cultivation of cells lead to changes in morphology of the cells. This is likely to explain the higher radioresistance of cells growing in 3D compared to cells growing in 2D cell culture. Whole genome gene expression is performed to determine genes involved in changes of cell moroholgy and radiore...
ORGANISM(S): Homo sapiens 
2010-07-30 | E-GEOD-17347 | biostudies-arrayexpress
ProteomicsDifferential protein and glycan packaging into extracellular vesicles in response to 3D gastric cancer cellular organization
Alterations of the glycosylation machinery are a common event in cancer that leads to the synthesis of aberrant glycan structures by tumor cells. Extracellular vesicles (EVs) play a modulator role in cancer communication and progression, and interestingly, several tumor-associated glycans have alrea...
ORGANISM(S): Homo sapiens (Human) 
2023-10-24 | PXD035650 | Pride
Glycosylation 3d Evs Gastric cancer 
ProteomicsRegulation of mammalian 3D genome organization and histone H3K9 dimethylation by H3K9 methyltransferases
Histone H3 lysine 9 dimethylation (H3K9me2) is a highly conserved silencing epigenetic mark. Chromatin marked with H3K9me2 forms large domains in mammalian cells and overlaps well with lamina-associated domains and the B compartment defined by Hi-C. However, the role of H3K9me2 in 3-dimensional (3D)...
ORGANISM(S): Mus musculus (Mouse) 
2021-08-05 | PXD024756 | Pride
Histone h3 methylation 
Genomics3D genome in CRPC
3D genome in CRPC
PRJEB29051 | ENA
UnknownThe 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions.
Not available
S-EPMC6172833 | biostudies-literature
TranscriptomicsGBS-based genomic characterization of a wheat–Thinopyrum 3J(3D) chromosome substitution line (GLA3)
A wheat–Thinopyrum chromosome substitution line (GLA3) was characterized at the genomic level using genotyping-by-sequencing (GBS). In the GLA3 line, a Thinopyrum-derived group 3 chromosome (3J) replaces wheat chromosome 3D. To confirm the chromosomal composition, identify the homoeologous relations...
ORGANISM(S): Triticum aestivum 
2026-05-19 | E-MTAB-17093 | biostudies-arrayexpress
GenomicsLoss of neuronal 3D chromatin organization causes transcriptional and behavioral deficits related to serotonergic dysfunction [ChIP-seq]
The interior of the neuronal cell nucleus is a highly organized 3-dimensional (3D) structure in which regions of the genome that are millions of bases apart participate in specialized sub-structures with dedicated functions. To investigate neuronal chromatin organization and dynamics in vivo, we gen...
ORGANISM(S): Mus musculus 
2014-07-18 | E-GEOD-56809 | biostudies-arrayexpress
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