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Series GSE41846 Query DataSets for GSE41846
Status Public on Jun 17, 2013
Title longitudinal expression profiling in whole blood of multiple sclerosis patients and controls [IFN_discovery dataset]
Organism Homo sapiens
Experiment type Expression profiling by array
Summary 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).
 
Overall design 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.
 
Contributor(s) Nickles D, Oksenberg JR, Baranzini SE
Citation(s) 23748426, 25721402
Submission date Oct 26, 2012
Last update date Apr 06, 2015
Contact name Sergio E Baranzini
E-mail(s) sebaran@cgl.ucsf.edu
Organization name University of California San Francisco
Department Neurology
Street address 675 Nelson Rising Lane, Room S-215
City San Francisco
State/province CA
ZIP/Postal code 94158-2306
Country USA
 
Platforms (1)
GPL16209 Affymetrix Human Exon 1.0 ST Array [CDF: HuEx_1_0_st_v2_core_na31_hg19_HB20110919_noSNPs]
Samples (318)
GSM1025555 MS patient 41465.0001, Baseline visit
GSM1025556 MS patient 41465.0001, follow-up year 1 visit
GSM1025557 MS patient 600009.0001, Baseline visit
This SubSeries is part of SuperSeries:
GSE41850 Longitudinal expression profiling in whole blood of multiple sclerosis patients and controls
Relations
BioProject PRJNA178315

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE41846_RAW.tar 7.1 Gb (http)(custom) TAR (of CEL)
Processed data included within Sample table
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