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

Prior to quality control (QC) analysis, we pre-screened and preprocessed each dataset. Normalized raw data and the study design table were imported from the GEO databases (The data was assumed to be normalized by robust multi-array average, but in some cases the published study used an alternative normalization method). Where appropriate, the intensity values were log 2 transformation. Various experimental parameters such as time point, virus strain and number of replicates were extracted from the study design tables. Samples irrelevant to the main study design were marked for segregation or exclusion from our downstream analysis, but not excluded from quality assessment. These were classified as ''failing to meet treatment specification'' at the candidate filtering step. Studies that had a large number of missing intensity values (over 10%) were annotated and flagged.