Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Longitudinal expression profiling in whole blood of multiple sclerosis patients and controls

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Dorothee Nickles

PROVIDER: E-GEOD-41850 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Blood RNA profiling in a large cohort of multiple sclerosis patients and healthy controls.

Nickles Dorothee D Chen Hsuan P HP Li Michael M MM Khankhanian Pouya P Madireddy Lohith L Caillier Stacy J SJ Santaniello Adam A Cree Bruce A C BA Pelletier Daniel D Hauser Stephen L SL Oksenberg Jorge R JR Baranzini Sergio E SE

Human molecular genetics 20130606 20

Multiple sclerosis (MS) is the most common autoimmune disease of the central nervous system (CNS). It is characterized by the infiltration of autoreactive immune cells into the CNS, which target the myelin sheath, leading to the loss of neuronal function. Although it is accepted that MS is a multifactorial disorder with both genetic and environmental factors influencing its development and course, the molecular pathogenesis of MS has not yet been fully elucidated. Here, we studied the longitudin ...[more]

PMID: 23748426

Similar Datasets

longitudinal expression profiling in whole blood of multiple sclerosis patients and controls [IFN_replication dataset]

Project description:Multiple sclerosis is the most common autoimmune disease of the central nervous system. Studying whole blood RNA from a cohort of 195 MS patients and 66 healthy controls, we identified gene expression signatures for interferon treatment and disease status by microarray analysis. Blood was collected at multiple time points (up to 3 for patients, 2 for controls). Patients were either untreated or treated with Interferon. In total, 626 Affymetrix exon arrays were analyzed, split into discovery and replication data sets. This metadata file contains information on all samples processed in the replication data set (n=183) when we compared gene expression in untreated MS patients (n=27) to IFN treated patients (n=48). The following comparisons were made: untreated MS vs Controls (discovery and replication), untreated vs Interferon treated MS (discovery and replication). For each comparison, respective arrays were processed (background corrected and normalized) together, but seperate from other comparisons. The two time points for controls were averaged. For the first comparison, we report differentially expressed genes at an FDR cutoff of 0.1 at any of the three tested time points in MS patients in the discovery data set. For the second comparison, the FDR cutoff was 0.001. The respective genes were validated in the replication data set when they passed a nominal p-value cutoff of 0.05 at any of the three tested time points.

2013-06-17 | E-GEOD-41847 | biostudies-arrayexpress

longitudinal expression profiling in whole blood of multiple sclerosis patients and controls [MS vs Ctrl Replication dataset]

Project description:Multiple sclerosis is the most common autoimmune disease of the central nervous system. Studying whole blood RNA from a cohort of 195 MS patients and 66 healthy controls, we identified gene expression signatures for interferon treatment and disease status by microarray analysis. Blood was collected at multiple time points (up to 3 for patients, 2 for controls). Patients were either untreated or treated with Interferon. In total, 626 Affymetrix exon arrays were analyzed, split into discovery and replication data sets. This metadata file contains information on all samples processed in the replication data set (n=102) when we compared gene expression in untreated MS patients (n=27) to healthy controls (n=25). The following comparisons were made: untreated MS vs Controls (discovery and replication), untreated vs Interferon treated MS (discovery and replication). For each comparison, respective arrays were processed (background corrected and normalized) together, but seperate from other comparisons. The two time points for controls were averaged. For the first comparison, we report differentially expressed genes at an FDR cutoff of 0.1 at any of the three tested time points in MS patients in the discovery data set. For the second comparison, the FDR cutoff was 0.001. The respective genes were validated in the replication data set when they passed a nominal p-value cutoff of 0.05 at any of the three tested time points.

2013-06-17 | E-GEOD-41849 | biostudies-arrayexpress

longitudinal expression profiling in whole blood of multiple sclerosis patients and controls [MS vs Ctrl Discovery dataset]

Project description:Multiple sclerosis is the most common autoimmune disease of the central nervous system. Studying whole blood RNA from a cohort of 195 MS patients and 66 healthy controls, we identified gene expression signatures for interferon treatment and disease status by microarray analysis. Blood was collected at multiple time points (up to 3 for patients, 2 for controls). Patients were either untreated or treated with Interferon. In total, 626 Affymetrix exon arrays were analyzed, split into discovery and replication data sets. This metadata file contains information on all samples processed in the discovery data set (n=212) when we compared gene expression in untreated MS patients (n=62) to healthy controls (n=41). The following comparisons were made: untreated MS vs Controls (discovery and replication), untreated vs Interferon treated MS (discovery and replication). For each comparison, respective arrays were processed (background corrected and normalized) together, but seperate from other comparisons. The two time points for controls were averaged. For the first comparison, we report differentially expressed genes at an FDR cutoff of 0.1 at any of the three tested time points in MS patients in the discovery data set. For the second comparison, the FDR cutoff was 0.001. The respective genes were validated in the replication data set when they passed a nominal p-value cutoff of 0.05 at any of the three tested time points.

2013-06-17 | E-GEOD-41848 | biostudies-arrayexpress

longitudinal expression profiling in whole blood of multiple sclerosis patients and controls [IFN_discovery dataset]

Project description:Multiple sclerosis is the most common autoimmune disease of the central nervous system. Studying whole blood RNA from a cohort of 195 MS patients and 66 healthy controls, we identified gene expression signatures for interferon treatment and disease status by microarray analysis. Blood was collected at multiple time points (up to 3 for patients, 2 for controls). Patients were either untreated or treated with Interferon. In total, 626 Affymetrix exon arrays were analyzed, split into discovery and replication data sets. This metadata file contains information on all samples processed in the discovery data set (n=318) when we compared gene expression in untreated MS patients (n=62) to IFN treated patients (n=58). The following comparisons were made: untreated MS vs Controls (discovery and replication), untreated vs Interferon treated MS (discovery and replication). For each comparison, respective arrays were processed (background corrected and normalized) together, but seperate from other comparisons. The two time points for controls were averaged. For the first comparison, we report differentially expressed genes at an FDR cutoff of 0.1 at any of the three tested time points in MS patients in the discovery data set. For the second comparison, the FDR cutoff was 0.001. The respective genes were validated in the replication data set when they passed a nominal p-value cutoff of 0.05 at any of the three tested time points.

2013-06-17 | E-GEOD-41846 | biostudies-arrayexpress

Exon-level expression profiling of normal colonic mucosa samples.

Project description:These samples have been analyzed for global alternative splicing variation on exon-level expression data using the FIRMA algorithm. We have identified and described transcriptome instability as a genome-wide, pre-mRNA splicing related characteristic of solid cancers. This Series consists of 19 normal colonic mucosa samples from colorectal cancer patients, and is an amendment to a larger series of colorectal cancer and adjacent normal colonic mucosa samples analyzed for gene expression at the exon-level (GSE24550).

2014-08-13 | E-GEOD-42690 | biostudies-arrayexpress

Exon level expression profiling of colorectal cancer tissue samples (validation sample series).

Project description:Colorectal cancer is a heterogeneous disease molecularly characterized by inherent genomic instabilities, chromosome instability and microsatellite instability. In the present study we propose transcriptome instability as an analogue to genomic instability on the transcriptome level. Exon microarray data from two independent series of altoghether 160 colorectal cancer tissue samples was used for global alternative splicing detection using the FIRMA algorithm (aroma.affymetrix). The sample-wise amounts of these alternative splicing scores exceeding a defined threshold (deviating exon usage amounts) were summarized to provide the basis for description of transcriptome instability. This characteristic was shown to be associated with splicing factor expression levels and patient survival in both independent sample series. We analyzed genome-wide expression at the exon-level for two independent series of colorectal cancer tissue biopsies using the Affymetrix Human Exon 1.0 ST platform. This series of samples represents the validation series.

2011-05-19 | E-GEOD-24550 | biostudies-arrayexpress

Exon level expression profiling of colorectal cancer tissue samples

Project description:This SuperSeries is composed of the following subset Series: GSE24549: Exon level expression profiling of colorectal cancer tissue samples (test sample series). GSE24550: Exon level expression profiling of colorectal cancer tissue samples (validation sample series). Refer to individual Series

2011-05-19 | E-GEOD-24551 | biostudies-arrayexpress

Exon level expression profiling of colorectal cancer tissue samples (test sample series).

2011-05-19 | E-GEOD-24549 | biostudies-arrayexpress

Molecular signature of brain resident memory CD8+ T cells

Project description:Tissue resident memory (Trm) represent a newly described memory T cell population. We have previously characterized a population of Trm that persists within the brain following acute virus infection. Although capable of providing marked protection against a subsequent local challenge, brain Trm do not undergo recall expansion following dissociation from the tissue. Furthermore, these Trm do not depend on the same survival factors as the circulating memory T cell pool as assessed either in vivo or in vitro. To gain greater insight into this population of cells we compared the gene-expression profiles of Trm isolated from the brain to circulating memory T cells isolated from the spleen following an acute virus infection. Trm displayed altered expression of genes involved in chemotaxis, expressed a distinct set of transcription factors and overexpressed several inhibitory receptors. Cumulatively, these data indicates that Trm are a distinct memory T cell population disconnected from the circulating memory T cell pool and displaying a unique molecular signature which likely results in optimal survival and function within their local environment. 13 samples were analyzed: 5 replicates of memory OT-I CD8+.CD103- T cells isolated from the spleen of mice on day 20 p.i. with VSV-OVA. 5 replicates of memory OT-I CD8+CD103+ T cells isolated from the brain of mice on day 20 p.i. with VSV-OVA; and 3 replicates of memory OT-I.CD8+ CD103- T cells isolated from the brain of mice on day 20 p.i. with VSV-OVA

2012-08-29 | E-GEOD-39152 | biostudies-arrayexpress

Gene level expression profiling of colorectal cancer tissue samples (test sample series)

Project description:This series is part of a larger series (GSE24549) of colorectal cancer tissue samples analyzed for global gene expression. The expression measures were used to develope a gene signature for prediction of prognosis in stage II and III colorectal cancer. Gene expression profiling of colorectal cancer tissue samples for prognosis prediction.

2012-01-05 | E-GEOD-30378 | 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