Identification of Common Biological Pathways and Drug Targets Across Multiple Respiratory Viruses Based on Human Host Gene Expression Analysis

Smith, Steven B.; Dampier, William; Tozeren, Aydin; Brown, James R.; Magid-Slav, Michal

Once a comparison group passed the QC analysis filters, LSM values were calculated for each probe using Array Studio in order to reduce the number of false positives due to low probe intensity values. Probes within each of the filtered datasets were tested for biological and statistical relevance using the Array Studio implementation of fold change and statistical models, respectively. Specifically, to determine a probe's fold change expression when compared to control, the geometric mean of each probe's log 2 transformed intensity value within a treatment was generated, and then normalized to the corresponding control group's geometric mean. The treatment versus control data were fitted to a general linear model, and associated p-values for each probe were calculated using a modified t-test [96] . Thus, to be considered differentially expressed, each probe within a comparison group must have a p-value ,0.05 after general linear model test and a fold change in either direction of 1.5.