Consistent with this interpretation, most functional categories with a difference in enrichment between these networks are those related to genes localized in the nucleus, which is the main cell compartment with over-representation in BIOGRID.
Consequently most functional experiments with primary rat hepatocytes occur soon after seeding onto the substrate and rarely progress beyond 2 3 days.
A striking up-regulation of gene expression was observed at 6 h post-infection in most functional categories, consistent with bacteria readapting their energy production, intermediary metabolism, protein synthesis, and nucleotide biosynthesis.
Most functional representations associated with individual genes/proteins are derived from the curation of scientific papers [ 25] which focus on small numbers of genes making them highly idiosyncratic and often failing to capture the cooperative aspect of biological function.
BSL1 also has been shown to interact with BIN2, albeit most functional studies were done with BSU1, suggesting that BSL1 probably plays similar role as BSU1 in the brassinosteroid signaling pathway (Kim et al. 2009).
Most functional classes are consistent with stromal as opposed to tumour cell function (e.g., proteinaceous extracellular matrix P=2.37 × 10−08, extracellular matrix P=2.49 × 10−08, collagen triple helix repeat P=7.12 × 10−07), although genes known to be expressed in tumour epithelium were identified (e.g., GREM1).
Among the subscores, the bronchiectasis score correlated best with most functional measures, similar to the total score.
Remarkably, most functional classes of proteins with a significant conservation signal were highly specific for the signal within one group of domains, but not in other groups.
Most functional studies addressing enhancer interactions with Hairy have been performed with synthetic cis elements, however, Hairy direct regulation of ftz 5' and 3' enhancers has been reported, and we find that these enhancers are indeed bound by Hairy (Li and Arnosti 2011).
