Computational protocol: Preclinical evaluation of the PI3K/Akt/mTOR pathway in animal models of multiple sclerosis

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Protocol publication

[…] Expression datasets for disease and drug effects were obtained from the NCBI Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/). MESH terms “Multiple Sclerosis” and “Rapamycin” were used to identify potential datasets of interest and GSE29606 and GSE38645 were chosen for the analysis. The GEO2R web application was used to identify differentially expressed genes. In cases where multiple microarray probes mapped to the same NCBI GeneID, we chose the probes which showed the maximum variance. On each data set, we performed moderate t statistics to generate a list of up-regulated and down-regulated genes. We used a threshold of p < 0.05 and fold change > 1.5. The list of significantly up and down regulated genes for each comparison were considered for further analysis. […]

Pipeline specifications

Software tools GEO2R, GeneID
Databases GEO
Application Transcription analysis
Organisms Homo sapiens
Diseases Autoimmune Diseases, Demyelinating Diseases, Multiple Sclerosis, Wounds and Injuries, Neurodegenerative Diseases, Hereditary Central Nervous System Demyelinating Diseases
Chemicals Sirolimus