Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

49 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A transcriptional signature of fatigue derived from patients with primary SjÃ¶gren's Syndrome

ABSTRACT: Fatigue is a debilitating condition with a significant impact on patientsâ quality of life. Fatigue is frequently reported by patients suffering from primary Sjo Ìgrenâs Syndrome (pSS), a chronic autoimmune condition characterised by dryness of the eyes and the mouth. However, although fatigue is common in pSS, it does not manifest in all sufferers, providing an excellent model with which to explore the potential underpinning biological mechanisms. Whole blood samples from 131 fully-phenotyped pSS patients, stratified for the presence of fatigue, collected by the UK primary Sj Ìogrenâs Syndrome Registry were used for whole genome microarray. The resulting data were analysed both on a gene by gene basis and using pre-defined groups of genes. Finally, gene set enrichment analysis (GSEA) was used as a feature selection technique for input into a support vector machine (SVM) classifier. Classification was assessed using area under curve (AUC) of receiver operator characteristic and standard error of Wilcoxon statistic, SE(W). Contributor: The UK Primary SjÃ¶grenâs syndrome registry

ORGANISM(S): Homo sapiens

SUBMITTER: Simon Cockell

PROVIDER: E-GEOD-66795 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

DNA Methylation Patterns Associated with Fatigue in Primary SjÃ¶grenâs Syndrome

Project description:Genome-wide analysis of DNA methylation profiles from patients with SjÃ¶gren's syndrome with high versus low fatigue levels using the Illumina Infinium HumanMethylation450 Beadchip array. Background Chronic fatigue is a common, disabling, and poorly understood phenomenon. Recent studies indicate that epigenetic mechanisms may be involved in the expression of fatigue, a prominent feature of primary SjÃ¶grenâs syndrome (pSS). The aim of this study was to investigate whether DNA methylation profiles of whole blood are associated with fatigue in patients with pSS. Methods 48 pSS patients with high (n=24) or low (n=24) fatigue as measured by a visual analogue scale were included. Genome-wide DNA methylation was investigated using the Illumina HumanMethylation450 BeadChip array. Case-case study including SjÃ¶gren's patients with high fatigue (n=24) and patients with low fatigue levels (n=24)

2015-12-04 | E-GEOD-75679 | biostudies-arrayexpress

Whole-Blood gene expression profiling in primary Sjögren's Syndrome and healthy controls

Project description:Investigating differential gene expression between clinical phenotypes in primary Sjögren's Syndrome using matched healthy controls as a further comparator group. Samples are derived from the UK Primary Sjögren's Syndrome Registry (UKPSSR)

2019-09-30 | E-MTAB-8277 | biostudies-arrayexpress

DNA Methylation Patterns Associated with Fatigue in Primary Sjögren’s Syndrome

Project description:Genome-wide analysis of DNA methylation profiles from patients with Sjögren's syndrome with high versus low fatigue levels using the Illumina Infinium HumanMethylation450 Beadchip array. Background Chronic fatigue is a common, disabling, and poorly understood phenomenon. Recent studies indicate that epigenetic mechanisms may be involved in the expression of fatigue, a prominent feature of primary Sjögren’s syndrome (pSS). The aim of this study was to investigate whether DNA methylation profiles of whole blood are associated with fatigue in patients with pSS. Methods 48 pSS patients with high (n=24) or low (n=24) fatigue as measured by a visual analogue scale were included. Genome-wide DNA methylation was investigated using the Illumina HumanMethylation450 BeadChip array.

2015-12-04 | GSE75679 | GEO

A transcriptional signature of fatigue derived from patients with primary Sjögren's Syndrome

Project description:Fatigue is a debilitating condition with a significant impact on patients’ quality of life. Fatigue is frequently reported by patients suffering from primary Sjo ̈gren’s Syndrome (pSS), a chronic autoimmune condition characterised by dryness of the eyes and the mouth. However, although fatigue is common in pSS, it does not manifest in all sufferers, providing an excellent model with which to explore the potential underpinning biological mechanisms.

2015-12-31 | GSE66795 | GEO

Zinc sensing by metal-responsive transcription factor 1 (MTF1) controls metallothionein and ZnT1 expression to buffer the sensitivity of the transcriptome response to zinc

Project description:Only a small number of genes are known direct targets of the zinc-responsive transcription factor MTF1; therefore, the aim of this study was to gain a more complete understanding of the MTF-1 regulated zinc-responsive component of the transcriptome. A targeted siRNA was used to deplete MTF1 expression in the human intestinal cell line Caco-2. We predicted that the response to zinc of direct MTF1 target genes would be abrogated by MTF1 knockdown. Surprisingly, a greater number of genes were regulated by zinc following MFT1 knockdown, and most genes that responded to zinc under both control and MTF1-depleted conditions had an augmented response in the latter condition. Exceptions were the zinc effluxer ZnT1 and a suite of metallothionein genes, suggesting that responses of other genes to zinc are usually buffered by increases in these proteins. We propose that MTF1 heads a hierarchy of zinc sensors, and through controlling the expression of a raft of metallothioneins and other key proteins involved in controlling intracellular zinc levels (e.g. ZnT1) alters zinc buffering capacity and total cellular zinc content. We tested and validated this model by overexpressing metallothionein and observing the predicted curtailment in response of the zinc-repressed SLC30A5 (ZnT5) promoter. The model provides the framework for an integrated understanding of cellular zinc homeostasis. Because MTs can bind metals other than zinc, this framework links with overall cellular metal homeostasis. Gene expression profiling by Illumina BeadArray of the effects of ZNF658 gene knockdown by siRNA. 2 different siRNAs were used, with appropriate non-targetting controls. All experiments were carried out in triplicate.

2016-02-24 | E-GEOD-76510 | biostudies-arrayexpress

Gene expression analysis of cancer-related fatigue in whole blood from breast cancer survivors

Project description:Cancer-related fatigue is one of the most frequent complaints among breast cancer survivors, with a major negative impact on general life. However, the etiology behind this syndrome is still unraveled. Gene expression analysis was performed on whole blood samples from breast cancer survivors classified as either fatigued or non-fatigued at two consecutive time points. The analysis identified several gene sets concerning plasma and B cell pathways as different between the fatigue and non-fatigue groups, suggesting that a deregulation in these pathways might underlie the fatigue syndrome. The fatigue group also showed a higher mean level of leucocytes, lymphocytes and neutrophiles compared with the non-fatigue group, thus further implicating the immune system in the biology behind the fatigue syndrome. Keywords: Blood RNA and late side effects Breast cancer survivors treated with adjuvant radiotherapy at The Norwegian Radium Hospital between 1998 and 2002 were invited to participate in a study assessing late treatment effects in breast cancer survivors. In the present study, gene expression analysis was performed on whole blood samples from breast cancer survivors with and without persistent fatigue, to look for different expression patterns that might shed light on the biology behind cancer-related fatigue.

2009-07-01 | E-GEOD-14786 | biostudies-arrayexpress

Transcriptome analysis of circulating monocytes in QFS and CFS compared to various control groups

Project description:Transcriptomes of circulating monocytes in Q fever fatigue syndrome (QFS) patients, chronic fatigue syndrome (CFS) patients, asymptomatic Q fever seropositive controls and healthy controls

2019-05-06 | GSE130353 | GEO

Microarray analysis of epithelial and fibroblast cells in chronic rhinosinusitis

Project description:Chronic rhinosinusitis without polyps (CRSsNP) is typified by inflammation of the sinonasal epithelium and the development of fibrosis. The precise pathophysiology of this common condition remains elusive. Here we aim to investigate the transcriptome (RNA transcripts in the cell) of the component nasal epithelial and fibroblast cells in CRSsNP and health to identify if there are clusters of differentially expressed genes as possible novel CRS therapeutic targets. Gene expression profiling by Illumina BeadArray of primary nasal epithelial and fibroblast cells in heatlh and chronic sinusitis. Samples from consenting human donors (Epithelial Case, n=13, Epithelial Control, n=11, Fibroblast Case, n=12, Fibroblast Control, n=12).

2015-12-31 | E-GEOD-69093 | biostudies-arrayexpress

Gene expression analysis of cancer-related fatigue in whole blood from breast cancer survivors

2009-07-01 | GSE14786 | GEO

Transcription profiling by array of parotid tissue from Primary Sjögren’s Syndrome and controls

Project description:Primary Sjögren’s syndrome (pSS) is a chronic autoimmune disease with complex etiopathogenesis. Here we use Affymetrix U133 plus 2.0 microarray gene expression data from human parotid tissue. Parotid gland tissues were harvested from 17 pSS and 14 14 non-pSS sicca patients and 18 controls. The data were used in the following article: Nazmul-Hossain ANM, Pollard RPE, Kroese FGM, Vissink A, Kallenberg CGM, Spijkervet FKL, Bootsma H, Michie SA, Gorr SU, Peck AB, Cai C, Zhou H, Horvath S, Wong DTW (2012) Systems Analysis of Primary Sjögren’s Syndrome Pathogenesis in Salivary Glands: Comparative Pathways and Molecular Events in Humans and a Mouse Model. Parotid gland tissues were harvested from 17 pSS and 14 non-pSS sicca patients and 18 controls.

2012-09-06 | E-GEOD-40611 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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