When AtPAPS3 and AtPCFS1+AtPCFS5 are removed from the overall interaction network, very little changes as far as the overall topology is concerned.
Overall, the interaction network contained 26 proteins and 97 interactions (edges) after filtering as described in the 'Materials and methods'.
Even if any valid kernel K can be applied to compute the above proposed scores, in the context of network-based gene prioritization, we used random walk kernels [53], since they can capture the similarity between genes, taking into account the topology of the overall functional interaction network.
To better understand the significance of the highly-ranked TFs, modules, and the overall TF interaction network, all 2,634 proteins (output from BIOMAP) were analysed using MetaCoreTM for their significance in various pathways from the original bait list (39 pathways) and the literature augmented data-generated list (286 pathways).
Given that about 25 000 protein-coding genes in the human genome can occur in multiple splice forms, the number of genes integrated in our cellular signaling model is still a fraction (ca. 2.5%) of the overall cellular interaction network; moreover, it is as yet devoid of aspects of the immune system and metabolism, such as cytochrome c, as well as the human microbial milieu.
Recent advances in high-throughput methods have provided us with a first glimpse of the overall structure of molecular interaction networks in biological systems.
These reductionist approaches are intrinsically unable to fully capture the overall complexity of molecular interaction networks.
The salt bridge interactions of the matrix network are highly conserved [15], [37] and braced by glutamine residues to increase the overall interaction energy of the network to 3.5 in the qualitative measure introduced earlier [16], [21].
However, removal of these seven nodes from the overall polyadenylation factor interaction network does not change the overall nature of the network in a fundamental way.
Our analysis of E. coli K12 as a target genome indicated that the selection of reference organisms had a substantial effect on the overall properties of predicted protein interaction networks.
