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ProteomicsMapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning
Most genetic variants in the human genome reside in non-coding regions, where they can perturb regulatory elements, influence gene expression, and contribute to various phenotypes and diseases. However, identifying such functionally relevant genetic variation remains challenging. Here we integrate p...
ORGANISM(S): Homo sapiens (Human) 
2026-04-22 | PXD069116 | Pride
Lc-msms Non-coding variants Deep learning 
UnknownVariability of the Human Serum Metabolome over 3 Months in the EXPOsOMICS Personal Exposure Monitoring Study.
Not available
S-EPMC10469440 | biostudies-literature
ProteomicsIntegrative multi-omics analysis of intestinal organoid differentiation
Intestinal organoids accurately recapitulate epithelial homeostasis in vivo, thereby representing a powerful in vitro system to investigate lineage specification and cellular differentiation. Here, we applied a multi-omics framework on stem cell enriched and -depleted mouse intestinal organoids to o...
ORGANISM(S): Mus musculus (Mouse) 
2018-06-25 | PXD009700 | Pride
Adult intestinal stem cells Organoids Hnf4g Enterocytes Systems biology 
MetabolomicsLactate controls cancer stemness and plasticity through epigenetic regulation.

Tumours arise from uncontrolled cell proliferation driven by mutations in genes that regulate stem cell renewal and differentiation. Intestinal tumours, however, retain some hierarchical organization, maintaining both cancer stem cells (CSCs) and cancer differentiated cells (CDCs). This heterogen...

2025-05-28 | MTBLS11849 | MetaboLights
ProteomicsDynamic regulatory grammar of human promoters uncovered by MPRA-trained deep learning
One of the major challenges in genomics is to build computational models that accurately predict genome-wide gene expression from the sequences of regulatory elements. Promoters play a key role in gene regulation, yet their regulatory logic remains incompletely understood. Here, we present PARM, a c...
ORGANISM(S): Homo sapiens (Human) 
2026-01-14 | PXD072017 | Pride
Synthetic biology Massively parallel reporter assay Convolutional neural network Promoter Gene regulation Transcription factor Deep learning in genomics. Genetics 
ProteomicsIntegrated Multi-Omics Reveal Polycomb Repressive Complex 2 Restricts Human Trophoblast Induction
Human naive pluripotent stem cells have unrestricted lineage potential. Underpinning this property, naive cells are thought to lack chromatin-based lineage barriers. However, this assumption has not been tested. Here, we apply multi-omics to comprehensively define the chromatin-associated proteome, ...
ORGANISM(S): Homo sapiens (Human) 
2022-05-06 | PXD028162 | Pride
Histone post-translational modifications Hpscs Trophoblast Prc2 Lc-ms/ms 
MetabolomicsGeographic variation of mutagenic exposures in kidney cancer genomes

International differences in the incidence of many cancer types indicate the existence of carcinogen exposures that have not been identified by conventional epidemiology yet potentially make a substantial contribution to cancer burden1. This pertains to clear cell renal cell carcinoma (ccRCC), fo...

2024-03-26 | MTBLS9394 | MetaboLights
ProteomicsIdentification of FAME (Factor Associated with Metabolism and Energy) interactome
Using comparative genomics, we discovered that a previously uncharacterized gene (1700011H14RIK/C14ORF105/CCDC198) hereby named FAME (Factor Associated with Metabolism and Energy) shows an unusually high rate of evolutionary divergence in birds and mammals. By comparing SNVs, we identified gene-flow...
ORGANISM(S): Homo sapiens (Human) 
2023-07-20 | PXD039259 | Pride
Fame Co-ip Hek293 
ProteomicsLow endothelial cell FAK expression reduces pancreatic ductal adenocarcinoma liver metastasis after gemcitabine treatment
Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive cancers with a high level of liver metastasis. Despite substantial advances, resistance to therapy, including gemcitabine, is still a major obstacle to improved progression free survival. Recent studies have indicated that endothe...
ORGANISM(S): Mus musculus (Mouse) 
2023-03-10 | PXD021542 | Pride
Endothelium Chemotherapy Focal adhesion kinase Tumour models Resistance Gemcitabine Phosphoproteomics Metastasis Pancreatic ductal adenocarcinoma Lc-ms/ms 
ProteomicsCerebrospinal fluid proteomics in recent-onset Narcolepsy type 1 reveals activation of the complement system
Narcolepsy type 1 (NT1) is a rare, chronic and disabling neurological disease causing excessive daytime sleepiness and cataplexy. NT1 is characterized pathologically by an almost complete loss of neurons producing the orexin neuropeptides in the lateral hypothalamus. Genetic and environmental factor...
ORGANISM(S): Homo sapiens (Human) 
2023-04-06 | PXD041093 | Pride
Neuroimmunology Coagulation system Cerebrospinal fluid Complement system Immune response Narcolepsy type 1 Proteomics 
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