Additional file 6: of Human Alzheimer’s disease gene expression signatures and immune profile in APP mouse models: a discrete transcriptomic view of Aβ plaque pathology

Table S3. Human AD translational transcriptomic profiling. Comparative gene network analysis was carried out from the mouse models used (tgCRND8 and Tg2576 models) in our study with that of: 1) Human aging (up-regulated) 2) Human aging (down-regulated) 3) Human inflammation signature 3) ITIM/ITAM-domain associated network signature 3) Mouse microglial gene signature (Barres et al., 2013) and 4) Mouse disease-associated microglia or DAM gene signature (Keren-Sheul et al., 2017). Differentially expressed genes were identified by Pearson correlation or T-test using Matlab R2010b (Mathworks). A. p-value cutoff of < 0.001 was used to identify differentially expressed genes. The FDR corresponding to this p-value is given in each of the comparisons to convey relative signature confidence. Set annotation analysis was performed by comparing input sets to GeneGo ( www.genego.com ), Ingenuity ( www.ingenuity.com ) and KEGG ( www.genome.jp/kegg/ ) pathway sets. Bonferroni corrected hypergeometric p-values (expectation (e)-values) of less than 0.1 were considered significant overlap between sets. (XLSX 26 kb)