Additional file 7: of Human Alzheimer’s disease gene expression signatures and immune profile in APP mouse models: a discrete transcriptomic view of Aβ plaque pathology

Table S4. Laser captured plaque transcriptomic signature. RNAseq data of laser-capture microscopy of TgCRND8 plaques versus non-plaque tissue as outlined in schematic in Fig. 2. Data shows statistical analysis of TgCRND8 plaques versus non-plaque tissue at 6 months of age (p-value) and log10 analysis of the ratio of TgCRND8 plaques versus non-plaque tissue. 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. (XLS 1410 kb)