Molecular Characterization of Transcriptome-wide Interactions between Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus and Porcine Alveolar Macrophages in vivo

Zhou, Ping; Zhai, Shanli; Zhou, Xiang; Lin, Ping; Jiang, Tengfei; Hu, Xueying; Jiang, Yunbo; Wu, Bin; Zhang, Qingde; Xu, Xuewen; Li, Jin-ping; Liu, Bang

The raw data (Affymetrix GeneChip Scanner 3000) was converted to gene signal files by MAS 5.0 (Microarray Suite Version 5.0, Affymetrix). The data points were normalized between slides using the quantile normalization method used by Bolstad et al. [16] . The differentially expressed genes were selected using the SAM (Significance Analysis of Microarrays) package (http://www-stat.stanford.edu/~tibs/ SAM/), and the false discovery rate (FDR) values were generated using permutations of the repeated measurements to estimate the percentage of genes identified by chance. In the experiment, SAM settings were adjusted for a two class paired analysis, using one hundred permutations to calculate the differentially expressed gene list. The fold-change of 1.5 and a false discovery rate of approximately 5% were set as a threshold. All data are MIAME compliant and have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE22782 (http://www.ncbi.nlm.nih.gov /geo/query/acc.cgi?acc=GSE22782). Differential gene expressions were performed for hierarchical cluster (Ver.3.0) and TreeView (Ver.1.60) analyses [17] . The functional annotation of differentially expressed genes was performed by the DAVID (The Database for Annotation, Visualization and Integrated Discovery) gene annotation tool (http://david.abcc.ncifcrf.gov/) [18] , as well as by referring to a previous work [19] .