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

For each comparison group, the differentially expressed probes were mapped to their corresponding genes, and then a p-value was assigned for each pathway map using the software GeneGo (accessed June 2011). Next, the comparison group's significant pathway lists were combined to find the union of all significant pathways (that is, the combined pathway list where all treatment groups have at least one significant pathway). A total of 459 out of the approximately 650 pathway maps available in MetaBase were determined to be significant. Comparison groups having ,5% significant pathways of the total significant pathways (that is, comparison groups containing less than 23 significant pathways) lead to the exclusion of eleven comparison groups from the union list. Excluded groups were: HRV at 8 hours (eliminating one comparison group from GSE11348), HRV at 72 hours (eliminating one comparison group from GSE17156), both strains of FLU at 1 hour and 3 hours each and another strain at 6 hours (eliminating three comparison groups from GSE18816), RSV at 24 hours (eliminating all comparison groups from GSE24132), CMV at 24 and 72 hours (eliminating all comparison groups from GSE24434 [27] ), and FLU at 8 hours (eliminating all comparison groups from GSE24533 [28] ). At the end of the final step in our filtering process, a total of 15 datasets, or 28 comparison groups remained (Tables 1, S1 and S2).