Alzheimer's Disease Transcriptome Analysis

Using 833 brain tissue samples in the GEO database were analyzed, including 537 AD brain tissue samples and 296 control samples. The expression profiles of the GSE125583, GSE118553, GSE5281, GSE122063, and GSE157239 were download from the GEO database (http://www.ncbi.nlm.nih.gov/geo/) (Barrett et al., 2013 (link)). GSE125583 included 219 AD and 70 controls of fusiform gyrus tissue samples, which were obtained based on the GPL16791 platform (Srinivasan et al., 2020 (link)). GSE118553 included 167 AD and 100 controls of the cerebellum, entorhinal cortex, frontal cortex, and temporal cortex tissue samples, which were obtained based on the GPL10558 platform (Patel et al., 2019 (link)). Of these, 134 asymptomatic AD patients were excluded. GSE5281 obtained 87 AD and 74 control brain tissue samples of the following brain regions: the entorhinal cortex, hippocampus, medial temporal gyrus, superior frontal gyrus, posterior cingulate cortex, primary visual cortex, and middle temporal gyrus, based on the GPL570 platform (Liang et al., 2007 (link); Readhead et al., 2018 (link)). GSE122063 was obtained using the GPL16699 platform and included the frontal and temporal cortices from 56 AD and 44 healthy brain tissue samples, while 36 vascular dementia samples were excluded (McKay et al., 2019 (link)). The temporal cortex of eight AD patients and eight controls were obtained from GSE157239, based on the GPL21572 platform.
The expression profile of GSE125583 was normalized using the “Variance Stabilizing Transformation” function of the DESeq2 package. The expression profile of GSE118553 was normalized by “lumiExpresso” function of the Lumi package. The expression profiles of GSE5281 and GSE157239 were normalized using the “RMA” function of Affy package. Moreover, expression profile of GSE122063 was normalized using the limma package.