We obtained PPIs for the seeds using different public PPI databases: DIP [ 22], IntAct [ 23] and MINT [ 24] databases.
Using different repositories of annotated PPIs, a HF-related PPI network was assembled.
In this study, we examined a link between neurogenesis and PPI using different animal models and exploring the possibility of postnatal manipulation of neurogenesis affecting PPI, since gene-deficient mice show biological disturbances from prenatal stages.
This result is consistent with the findings of He and Zhang [11] and Yu et al. [12], where they found a relatively weak, yet significant positive association between fitness pleiotropy and PPI degree, using different datasets.
Cytoscape [ 60] allows users to build a customized pipeline to analyze PPI data by using different plug-ins and annotation tools, but the effective use of Cytoscape requires a thorough understanding of the tools and plug-ins available and expertise in organizing and interpreting the output.
We have implemented and tested HubAlign using quite a few PPI networks and evaluated the resultant alignments using different performance metrics.
Among SVMs using different types of features individually, GO annotation gives the best performance with AUC of 0.830, followed by PPI (AUC 0.767) and Pfam (AUC 0.706) features.
Using different datasets and techniques, Yook and Pandey both found correlation between the functional roles and topological structure, indicating that PPI networks are functionally organized [ 27, 28].
The conventional homology-based prediction strategy uses different template PPIs for the prediction: if a human protein A interacts with a human protein B in a template PPI, and the human protein B has a homolog B' identified in M.tuberculosis H37Rv, then it predicts that the human protein A and the M.tuberculosis H37Rv protein B' interact with each other.
By carrying out a series of reactions using different, but related, partially double stranded substrates we have observed several factors that influence the ability of the enzyme to remove terminal primer bases in the presence of PPi.
