Figure 1.
Condensed networks of bottlenecks and functional clusters.
A network was inferred from the macrophage innate immune compendium (A), or the blood- (B) or brain-(C) derived transcriptome from the stroke study. Bottlenecks (circles) were identified based on topological betweenness and clusters (squares) were assessed for statistical enrichment in gene ontology functional categories versus genes in the rest of network using the hypergeometric test. Shared functions are indicated by cluster color: orange, immune related/stress response; pink, signaling; green, cell cycle/mitosis. Clusters are labeled with most enriched functional category followed by the negative exponent of the p-value for enrichment. Edges are colored red to indicate that the bottleneck is a member of the cluster that it links to, and red to indicate that the bottleneck is linked to the cluster. Note that not all bottlenecks, clusters or relationships between the two are present in this representation (see text).
Table 1.
Shared bottlenecks between three inferred networks.
Table 2.
Shared neighbors of Ifit1 in three inferred networks.
Figure 2.
Silencing Ifit1 suppresses LPS activation of Usp18 and M×1.
siRNA against Ifit1 or a negative control were introduced into RAW264.7 macrophages by transfections and the macrophages were treated with 1 ng/mL of LPS. Expression of Ifit1 (A), Usp18 (B) and M×1 (C) were measured by RT-PCR at 3 hours post-LPS treatment. The results show that Ifit1 exerts a positive regulatory effect on Usp18 and M×1.