E-GEOD-41847 - longitudinal expression profiling in whole blood of multiple sclerosis patients and controls [IFN_replication dataset]

Released on 17 June 2013, last updated on 24 June 2013
Homo sapiens
Samples (183)
Array (1)
Protocols (5)
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.
Experiment type
transcription profiling by array 
Dorothee Nickles <dorothee.nickles@ucsf.edu>, Jorge R Oksenberg, Sergio E Baranzini
Blood RNA profiling in a large cohort of multiple sclerosis patients and healthy controls. Nickles D, Chen HP, Li MM, Khankhanian P, Madireddy L, Stacy CJ, Santaniello A, Cree BA, Pelletier D, Hauser SL, Oksenberg JR, Baranzini SE. , Europe PMC 23748426
Investigation descriptionE-GEOD-41847.idf.txt
Sample and data relationshipE-GEOD-41847.sdrf.txt
Processed data (1)E-GEOD-41847.processed.1.zip
Array designA-GEOD-16209.adf.txt