Supplementary Figure 4: Integration of DEGs with interactome and bibliome data. | Nature Immunology

Supplementary Figure 4: Integration of DEGs with interactome and bibliome data.

From: Molecular signatures of antibody responses derived from a systems biology study of five human vaccines

Supplementary Figure 4

(a) Illustration of the network integration method. DEGs from a vaccine study are connected by their links in the Interactome or Bibliome. Additional “linker” genes are then included based on their significant association to the DEGs (see Method for details). (b) Numbers of upregulated DEGs in common to 1 to 5 vaccine datasets. (c) Numbers of genes in the integrated network, and numbers of genes in common to 1 to 5 vaccine datasets. (d) The genes in common between MCV4 network and TIV network are highly expressed in plasma cells. As all genes are ranked by their expression level in sorted plasma cells (the color bar, according to data in Abbas et al 2009, PLoS ONE, 4:e6098), the ranks of MCV4/TIV common genes are indicated by the horizontal bars. (e) A subnetwork that is common between YF-17D and LAIV, enriched for TCR signaling pathway and interferon response genes. Genes in dark gray: DEGs as in (b), light gray: “linker” genes that have p < 0.05 in YF-17D transcriptomic data. (f) Genes enriched in the “immune systems development” GO category from Figure 3c.

Back to article page