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

After querying the GEO database and prescreening for obvious non-candidate datasets such as those not associated with human array platforms, there were at least 23 datasets associated with at least one of the twelve respiratory viruses. However, after considering all conditions for GEO dataset candidacy, at least four of these datasets were excluded. In one case, an ADENO dataset (GSE1291 [PMID unpublished]) had less than three samples per treatment group, as did a COX (GSE712 [PMID unpublished]) and a CMV (GSE19345 [24] ) dataset. As another example, a CMV dataset (GSE675 [25] ) lacked a healthy/control treatment group. Additionally, at least four datasets had some comparison groups that did not fit the filters for inclusion. For instance, an HRV (GSE13396) dataset's original study design was to observe differences in HRV infectivity between asthmatic and non-asthmatic patients. The asthmatic comparison group data were eliminated from the analysis because of potential difficulties in distinguishing between host inflammatory responses due to viral infections from those associated with chronic asthma. Similarly, a combined FLU, HRV and RSV dataset (GSE17156) contained two main patient groups. One group was classified as developing symptoms after exposure to a single virus under study, while the other group did not develop any symptoms after exposure. Only the group that developed symptoms for each of the three viruses was considered for further analysis and the asymptomatic group was omitted. In total, 19 GEO datasets, representing 42 unique comparisons (different time points and/or virus strains) were analyzed for quality because they met the four requirements for dataset candidacy.