Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Fine-mapping and functional studies highlight potential causal variants for rheumatoid arthritis and type 1 diabetes

ABSTRACT: We investigated whether variants fine-mapped for Rheumatoid Arthritis (RA) and Type 1 Diabetes overlap with open chromatin regions specifically after stimulation. We show that rs117701653, a potentially causal variant for RA near CD28, overlaps open chromatin regions only after stimulation. We futhermore observe a small increase in enhancer activity for this variant under stimulatory conditions using a luciferase assay. Reads were anonimized prior to upload.

ORGANISM(S): Homo sapiens

PROVIDER: GSE116497 | GEO | 2018/07/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Fine-mapping and functional studies highlight potential causal variants for rheumatoid arthritis and type 1 diabetes.

Project description: Not available

| S-EPMC6364548 | biostudies-literature

Comprehensive Epigenetic Landscape of Rheumatoid Arthritis Fibroblast-like Synoviocytes [WGBS]

Project description:Epigenetics is important in the pathogenesis of immune-mediated diseases like rheumatoid arthritis (RA). Here we show the first complete epigenomic characterization of RA fibroblast-like synoviocytes (FLS) by profiling histone modifications (H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3, H3K9me3), open chromatin, RNA expression and whole genome DNA methylation. To address the complex multidimensional relationship and reveal the epigenetic regulation of RA, we perform integrative analyses using a novel unbiased method to identify genomic regions with similar profiles. Epigenomically similar regions exist in RA cells are particularly associated with active enhancers and promoters as well as specific transcription factor binding motifs. Differentially marked genes are enriched for immunological and unexpected pathways, with “Huntington's Disease Signaling” identified as particularly prominent. We validate the relevance of this pathway to RA by showing that Huntingtin-interacting protein-1 regulates FLS invasion into matrix. This work establishes a high-resolution epigenomic landscape of RA and demonstrates the potential for integrative analyses to identify unanticipated therapeutic targets.

2018-04-30 | GSE112657 | GEO

Comprehensive Epigenetic Landscape of Rheumatoid Arthritis Fibroblast-like Synoviocytes [RNA-seq]

2018-04-30 | GSE112656 | GEO

Comprehensive Epigenetic Landscape of Rheumatoid Arthritis Fibroblast-like Synoviocytes [ChIP-seq]

2018-04-30 | GSE112655 | GEO

Comprehensive Epigenetic Landscape of Rheumatoid Arthritis Fibroblast-like Synoviocytes [ATAC-seq]

2018-04-30 | GSE112654 | GEO

The Regulatory Evolution of the Primate Fine-Motor System

Project description:In mammals, fine motor control is essential for skilled behavior, and is subserved by specialized subdivisions of the primary motor cortex (M1) and other components of the brain’s motor circuitry. We profiled the epigenomic state of several components of the Rhesus macaque motor system, including subdivisions of M1 corresponding to hand and orofacial control. We compared this to open chromatin data from M1 in rat, mouse, and human. We found broad similarities as well as unique specializations in open chromatin regions (OCRs) between M1 subdivisions and other brain regions, as well as species- and lineage-specific differences reflecting their evolutionary histories. By distinguishing shared mammalian M1 OCRs from primate- and human-specific specializations, we highlight gene regulatory programs that could subserve the evolution of skilled motor behaviors such as speech and tool use. Further, in order to predict candidate enhancers in additional species for which primary data was not available, we developed machine learning models trained on genome sequence across species.

2022-03-07 | GSE159815 | GEO

Gene expression analysis of SH-SY5Y neuroblastoma cells overexpressing ZNF423

Project description:We have identified ZNF423 (also known as Ebfaz, OAZ or Zfp423) as a component critically required for retinoic acid (RA)-induced differentiation. ZNF423 associates with the RARα/RXRα nuclear receptor complex and is essential for transactivation in response to retinoids. Down-regulation of ZNF423 expression by RNA interference in neuroblastoma cells results in a growth advantage and resistance to RA-induced differentiation, whereas overexpression of ZNF423 leads to growth inhibition and enhanced differentiation. Futhermore, we show that low ZNF423 expression is associated with poor disease outcome of neuroblastoma patients. To identify the other key pathways regulated by ZNF423 in human neuroblastoma, we expressed elevated levels of ZNF423 in SH-SY5Y cells and performed full genome gene expression analysis in these cells.

2009-04-29 | GSE14627 | GEO

Genome-wide analysis of chromatin accessibility in developing thymic Treg cells

Project description:We analyzed open chromatin regions in thymic Treg cells, their immediate precursors (CD25+ Foxp3-), and mature and semi-mature CD4 single positive cells. We wished to understand which chromatin regions become accessible in response to TCR-stimulation and then Foxp3 expression as Treg cells develop.

2019-08-19 | GSE134366 | GEO

Identifying causal variants by fine mapping across multiple studies.

Project description: Not available

| S-EPMC8491908 | biostudies-literature

Assessing the ability of various genomic features to prioritize causal non-coding variants associated with diseases and traits [MPRA]

Project description:Genome-wide association studies have associated thousands of genetic variants with complex traits and diseases, but pinpointing the causal variant(s) among those in tight linkage disequilibrium with each associated variant remains a major challenge. Here, we used seven experimental assays to characterize all common variants at the multiple disease-associated TNFAIP3 locus in three disease-relevant immune cell types, based on a set of features related to regulatory potential. Trait/disease-associated variants were enriched among SNPs prioritized based on either: (1) residing within CRISPRi-sensitive regulatory regions, or (2) localizing in a chromatin accessible region while displaying allele-specific reporter activity. Of the 15 trait/disease-associated haplotypes at TNFAIP3, 9 had at least one variant meeting one or both of these criteria, with 3 of these haplotypes having a single prioritized variant. 5 of the 9 prioritized variants were further supported by genetic fine-mapping in our and other studies. Our work provides evidence for the efficacy and limitations of strategies for prioritizing disease- and trait-associated genetic variants.

2020-02-11 | GSE136702 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data