Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA sequencing data of peripheral blood isolated from Korean patients with Crohn's disease.

ABSTRACT: We performed RNA sequencing to produce expression quantitative trait loci (eQTL) database of Crohn's disease patients. Using this eQTL data, we tried to determine the most functionally relevant genes at the established Crohn’s disease loci identified in genome-wide association studies (GWAS) involving Asian populations and to find novel disease-associated genes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE143507 | GEO | 2020/01/14

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA sequencing of peripheral blood mononuclear cells isolated from Korean patients with asthma

Project description:More than 200 asthma-associated genetic variants have been identified in genome-wide association studies (GWASs). Expression quantitative trait loci (eQTL) data resources can help identify causal genes of the GWAS signals, but it can be difficult to find an eQTL that reflects the disease state because most eQTL data are obtained from normal healthy subjects. We performed a blood eQTL analysis using transcriptomic and genotypic data from 436 Korean asthma patients. To identify asthma-related genes, we carried out colocalization and Summary-based Mendelian Randomization (SMR) analysis using the results of asthma GWASs and eQTL data. In addition, we compared the results of disease eQTL data and asthma-related genes with two normal blood eQTL data from Genotype-Tissue Expression (GTEx) project and a Japanese study. We identified 342,054 cis-eQTL and 2,931 eGenes from asthmatic eQTL analysis. We compared the disease eQTL results with GTEx and a Japanese study and found that 63.2 % of the 2,931 eGenes overlapped with the GTEx eGenes and 38.5 % with the Japanese eGenes. Following the integrated analysis of the asthmatic eQTL data with asthma GWASs, using colocalization and SMR methods, we identified 13 asthma-related genes specific to the Korean asthmatic eQTL data. We provided Korean asthmatic cis-eQTL data and identified asthma-related genes by integrating them with GWAS data. In addition, we suggested these asthma-related genes as therapeutic targets for asthma. We envisage that our findings will contribute to understanding the etiological mechanisms of asthma and provide novel therapeutic targets.

2023-03-08 | GSE226825 | GEO

eQTL in diseased colon tissue identifies novel target genes associated with IBD

Project description:Genome-wide association studies (GWAS) have identified over 300 loci associated with the inflammatory bowel diseases (IBD), but putative causal genes for most are unknown. We conducted the largest disease-focused expression quantitative trait loci (eQTL) analysis using colon tissue from 252 IBD patients to determine genetic effects on gene expression and potential contribution to IBD. Combined with two non-IBD colon eQTL studies, we identified 194 potential target genes for 108 GWAS loci. eQTL in IBD tissue were enriched for IBD GWAS loci colocalizations, provided novel evidence for IBD-associated genes such as ABO and TNFRSF14, and identified additional target genes compared to non-IBD tissue eQTL. IBD-associated eQTL unique to diseased tissue had distinct regulatory and functional characteristics with increased effect sizes. Together, these highlight the importance of eQTL studies in diseased tissue for understanding functional consequences of genetic variants, and elucidating molecular mechanisms and regulation of key genes involved in IBD.

2024-10-16 | GSE279302 | GEO

A functional genomics predictive network model identifies regulators of inflammatory bowel disease: Microarray Analysis of Human Blood and Intestinal Biopsy Samples from a Phase 2b, Double-blind, Placebo-controlled Study of Ustekinumab in Crohn's Disease

Project description:Microarray Analysis of Human Whole Blood and Intestinal Biopsy Samples from a Phase 2b, Multicenter, Randomized, Double-blind, Placebo-controlled, Parallel-group Study of Ustekinumab in Crohn’s Disease 329 Crohn's biopsies from multiple regions in the intestine of 87 anti TNFa refractory patients and blood samples from 204 patients at Week 0 prior to drug treatment are included in this study

2017-07-07 | E-GEOD-100833 | biostudies-arrayexpress

Colonic Crohn's left and right colon

Project description:Colonic Crohn's Disease from a single patient in remission with mild disease index

2020-08-24 | GSE141553 | GEO

Transcriptomic analysis reveals the dynamic changes of immune responses during the development of creeping fat in Crohn's disease

Project description:In Crohn's disease, creeping fat is the characteristic expansion of mesenteric adipose tissue wrapping around the inflamed intestine. Through a comparative transcriptomic analysis of creeping fat and normal-looking mesenteric adipose tissues from patients with Crohn's disease and non-Crohn's disease, we found that a dynamic transcriptional and cell compositional change occurs during the progression from non-Crohn's disease to Crohn's disease, and finally to creeping fat.

2023-09-06 | GSE227376 | GEO

Fibrotic signatures in Crohn's disease patients

Project description:This study investigates the presence of specific fibrosis-associated gene expression signatures in Crohn's disease patient biopsies.

2022-01-02 | GSE192786 | GEO

RNA-seq of 4 Crohn's disease and 4 control

Project description:mRNA-seq raw data of 4 Crohn's disease and 4 control from colon tissue

2022-01-01 | GSE164871 | GEO

Genes in Inflammatory Bowel Disease-Associated Risk Loci Demonstrate Genotype-, Tissue-, and Inflammation-Specific Patterns of Expression in Terminal Ileum and Colon Mucosal Tissue

Project description:With a greater understanding of the genetic risk variants associated with inflammatory bowel disease, there is a need to prioritize candidate genes within risk loci leading to the disease-SNP association. We created a custom NanoString probeset to capture 678 genes of interest in IBD (including 440 genes encoded within IBD risk loci and 15 housekeeping genes) - 22% of genes were not captured on traditional microarray platforms. Total RNA extracted from terminal ileum and colon tissues (uninflamed and inflamed) was used from patients with Crohn's disease and ulcerative colitis and healthy controls. We studied differential expression and performed an eQTL analysis to prioritize candidate genes within the risk loci.

2016-08-10 | GSE73094 | GEO

eQTL Analysis Identifies Novel Associations Between Genotype and Gene Expression in the Human Intestine (Illumina SNP)

Project description:Genome-wide association studies (GWAS) have been pivotal to increasing our understanding of intestinal disease. However, the mode by which genetic variation results in phenotypic change remains largely unknown, with many associated polymorphisms likely to modulate gene expression. Analyses of expression quantitative trait loci (eQTL) to date indicate that as many as 50% of these are tissue specific. Here we report a comprehensive eQTL scan of intestinal tissue.

2012-12-01 | GSE41238 | GEO

eQTL Analysis Identifies Novel Associations Between Genotype and Gene Expression in the Human Intestine (Expression)

2012-12-01 | GSE40292 | GEO