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

An illustration of the kernel density and Principle Component Analysis (PCA) plots generated during the QC analysis is shown in Figure 2 for GSE17156's RSV treatment (median of 141 hours post infection) and RSV control (baseline) groups. Additional QC analysis results including Median of Absolute Deviation (MAD) score plots and pair-wise correlation maps are shown in Figure S1 . Initially, all samples except GSM429279 showed acceptable kernel density (Figure 2a) , PCA (Figure 2c ), MAD score ( Figure S1a ) and pair-wise correlation ( Figure S1c ) plots. The sample GSM429279 was removed because: a) it did not conform to the kernel density of the other samples; b) it fell outside of the Hotelling T2 alpha threshold of 0.05 (represented by the superimposed elliptical on the PCA plot), and; c) it was an outlier in both the MAD score and pair-wise correlation plots. A second QC round was performed, which resulted in a further non-conforming sample, GSM429252, being discarded. Subsequent QC analysis generated acceptable results in kernel density (Figure 2b ), PCA (Figure 2d ), MAD score ( Figure S1b ), and pair-wise correlation ( Figure S1d ), thus this dataset passed our criteria for inclusion in the analysis.