Figure 6. Upstream analysis of time-varying B cell gene sets.

Ingenuity Pathways Analysis of significant time-varying genes of subjects S02 (5256 genes), S03 (1309 genes), S04 (2147 genes) was performed. Upstream modifiers with a Z-score of 2.0 or higher, indicating probable activation, are shown. Molecule sets downstream of these modifiers were not mutually exclusive. All three subjects showed probable activation by upstream cytokines typical of the germinal center reaction, including IL2, IL4, IL5, IL6 and CD40LG across days of peak response. Upstream modifiers unique to each subject suggested immunological differences. Of interest, late in the peak response of S04, IFN-related signaling molecules were identified. This could be the result of a previous innate-type stimulus such as interaction with plasmacytoid dendritic cells or viral DNA-initiated toll-like receptor activation. Our method identified dynamic gene regulation patterns with common as well as subject-specific upstream regulatory elements underlying the larger post-vaccine response.