As part of the "Core Analysis", IPA uses "network eligible molecules" (those molecules in the dataset that interact with other molecules in the IPA knowledgebase) as "seeds" to generate networks with a high degree of connectivity relative to all molecules in the knowledgebase. These networks provide insight to molecule connections and relationships that may not be detected by standard functional annotation methods. Using this approach, we compared the top two networks derived from each dataset containing DE microRNAs and their associated DE 120h targets (Table 4, S2 Fig). All datasets, except PFC 8hDEmiR/120hDEtargets, produced top networks in which ERK1/2 (mouse equivalent Mapk3, Mapk1) was a highly-connected member. These same networks contained other highly connected molecules, including Bcl2 (in AMY networks) and Srf (in PFC networks). In NAC and PFC, datasets utilizing targets from 0 and 8h microRNAs produced NF-kB-centered networks, while the same datasets in AMY generated networks sharing Smad3.
