1B). In this analysis, we project each significantly enriched gene set onto a radial plot. Gene sets that are closer to the center are more enriched in samples of the phenotype of interest (day seven, postvaccination). Gene sets that are similar Fulvestrant mouse to each other in terms of enrichment patterns will be clustered closely together. To further discern similarities between the gene sets, we connected gene sets with edges whose thickness is proportional to the fraction of genes that they have
in common. Groups of gene sets that both show a similar pattern of enrichment in the phenotype of interest and also share genes in common can be easily identified and are indicated by the arc on the perimeter of the radial plot. Using this method, we found that the
find more majority of the gene sets enriched in day seven samples formed a single highly connected cluster, suggesting that the top-scoring gene sets shared a predominant biological process. (Fig. 1B and Supporting Information Fig. 1). Analysis of the genes common to this cluster of gene sets again showed a striking overrepresentation of interferon response genes consistent with our previous work . Thus the gene sets that are correlated with day 7 post YF-17D status are associated with a single predominant biological process—the interferon response. These findings agree with the upregulation of individual interferon response genes in response to YF-17D vaccination previously observed , and suggest that a gene set based analytic approach can capture known biological features of the effect of vaccination with a live viral vaccine on PBMCs. Having Resminostat validated the analytical approach in samples from subjects vaccinated with YF-17D, we next applied gene set based analysis to a more challenging problem: identifying features that predict the antibody response to the inactivated influenza vaccine. We analyzed PBMC profiles from individuals vaccinated with the trivalent inactivated influenza vaccine (TIV) that
were collected prevaccination (day 0) and 7 days postvaccination . HAI titers for each subject were available prevaccination and 28 days postvaccination and were used as the outcome measure of vaccine response. We calculated the magnitude of antibody responses to the vaccine (HAI response) as the maximum difference between the HAI titer at day 28 and the baseline titer (day 0) for any of the three influenza strains contained in the vaccine. We classified the vaccinated subjects as low or high HAI responders based on whether or not a fourfold increase in titer occurred after vaccination. This criterion was based on our prior study , and on the US Food and Drug Administration Guidance for Industry document for this field . Using this criterion, 17 vaccines had a high HAI response and 7 had a low HAI response.