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)

补充表S4：激光捕获斑块转录组特征。本数据集为图2示意图中所述的TgCRND8小鼠斑块与非斑块组织的激光捕获显微切割（laser-capture microscopy）RNA测序（RNAseq）数据。数据包含6月龄TgCRND8小鼠斑块与非斑块组织的统计学分析（p值），以及二者表达量比值的log10转换分析。差异表达基因通过Matlab R2010b（Mathworks公司）的Pearson相关分析或T检验完成鉴定。本次分析以p值<0.001作为差异表达基因的筛选阈值。各比较组均附带对应此p值的错误发现率（False Discovery Rate, FDR），以体现特征置信度的相对高低。集注释分析通过将输入基因集与GeneGo（www.genego.com）、Ingenuity（www.ingenuity.com）及KEGG（www.genome.jp/kegg/）通路数据库进行比对完成。经Bonferroni校正的超几何检验p值（期望值，即e值）小于0.1时，即可认为两组间存在显著富集重叠。（XLS格式，文件大小1410 KB）