Network-based analysis provides system level relationship of molecules across different layers of regulatory controls of biological functions by integrating functional interactions with co-expression information.
Many functions such as nucleotide supply, functional interactions with Krebs cycle succinyl thiokinase, catabolism of short chain fatty acids [ 64, 65] and, more recently, GTP synthesis in relationship with iron homeostasis [ 66] have been proposed.
In light of evidence that the mammalian Tat-SF1 interacts with snRNPs and has functional interactions with P-TEFb, we considered the possibility that Cus2 and U2 could also affect transcription via interactions with the P-TEFb homologs.
To address whether a U2 snRNP function in transcription can be revealed through functional interactions with elongation factors, we performed a targeted genetic screen between CUS2 or the U2 snRNA and factors known to interact with the CDKs.
It has also been reported that the clock machinery has functional interactions with cell cycle regulators, so that changes in clock function result in uncontrolled cell cycle progression and cell proliferation [ 31].
Three members of this family – PGC1α, PGC1β and PRC – regulate several functions, including adaptative thermogenesis, glucidic metabolism, fatty acid oxidation and mitochondrial metabolism, via functional interactions with various transcriptional factors.
Perturbation of these pathways leads to diverse functional interactions with Myc: manifested as a RhoA-dependent synthetic lethality and Par6-dependent effects on the cell cycle.
Moreover, it has been shown that potentiation of FAE signaling at PPAR-α by FAAH inhibition can have various consequences, including functional interactions with signaling at CB1 receptors (Russo et al, 2007).
Recently it was proposed that the C-termini of Hfq subunits in Hfq6 complexes could be involved in functional interactions with other Hfq hexamers and/or nucleic acids.
Here, we sought to identify the domain of apoE that is responsible for its functional interactions with ABCA1 and the formation of apoE-rich HDL-like particles.
Motifs within the zebrafish LCR include CACCC, GATA, and NFE2 sites, suggesting functional interactions with known transcription factors but not the same LCR architecture.
