Despite the apparent conceptual simplicity of this approach, it is difficult to construct such networks, and most of the miRNA and TF mediated interactions are not yet well-characterized.
However, a certain type of linguistically mediated interaction is implicit in the equation, since children with different language proficiencies are expected to guide each other in the mutual process of language acquisition.
Of the four component effects, mediated interaction is considered intuitively most difficult to conceptualize and is usually thought of as blurring the separation of direct and indirect effects.
Thus, the current bottleneck in understanding RNA mediated interaction is the correct identification of genes that may be targeted by the numerous smRNAs in the cell.
The second example originates from biochemical sciences, in which mediated interaction is perhaps best illustrated by a process called auto-catalysis.
As PDZ domains interact with many proteins, understanding the regulatory mechanisms of PDZ-mediated interactions is important to gain insight into biological processes.
Ligand, hydrogen bonds and nearby residues are included and the list of possible water-mediated interactions is also available.
A standard test to validate Siglec-mediated interactions is to measure their susceptibility to sialidase treatment (Crocker et al., 2007).
It has been proposed that the relative stoichiometry of PABC-mediated interactions is the product of both direct binding competition and synergistic avidity effects [ 24].
When taken in conjunction with data on the interaction of vti1b with epsinR (Miller et al., 2007) and of VAMP7 with AP3 (Martinez-Arca et al., 2003b), the data shown here provide compelling evidence that the use of folded "regulatory" domain-mediated, rather than of the commonly used short, linear motif-mediated interactions, is the paradigm for sorting SNAREs into post-Golgi transport vesicles.
The final percentage is difficult to estimate as the total number of SLiM classes is unknown but taking into consideration that there are over 13 000 globular domain classes annotated in Pfam, the potential influence of SLiM-mediated interactions is prodigious.
