Interaction network

About: Interaction network is a research topic. Over the lifetime, 2700 publications have been published within this topic receiving 113372 citations.

Functional protein representations from biological networks enable diverse cross-species inference

Abstract: Transferring knowledge between species is key for many biological applications, but is complicated by divergent and convergent evolution. Many current approaches for this problem leverage sequence and interaction network data to transfer knowledge across species, exemplified by network alignment methods. While these techniques do well, they are limited in scope, creating metrics to address one specific problem or task. We take a different approach by creating an environment where multiple knowledge transfer tasks can be performed using the same protein representations. Specifically, our kernel-based method, MUNK, integrates sequence and network structure to create functional protein representations, embedding proteins from different species in the same vector space. First we show proteins in different species that are close in MUNK-space are functionally similar. Next, we use these representations to share knowledge of synthetic lethal interactions between species. Importantly, we find that the results using MUNK-representations are at least as accurate as existing algorithms for these tasks. Finally, we generalize the notion of a phenolog ('orthologous phenotype') to use functionally similar proteins (i.e. those with similar representations). We demonstrate the utility of this broadened notion by using it to identify known phenologs and novel non-obvious ones supported by current research.

Landscape Mapping of Functional Proteins in Insulin Signal Transduction and Insulin Resistance: A Network-Based Protein-Protein Interaction Analysis

Abstract: The type 2 diabetes has increased rapidly in recent years throughout the world. The insulin signal transduction mechanism gets disrupted sometimes and it's known as insulin-resistance. It is one of the primary causes associated with type-2 diabetes. The signaling mechanisms involved several proteins that include 7 major functional proteins such as INS, INSR, IRS1, IRS2, PIK3CA, Akt2, and GLUT4. Using these 7 principal proteins, multiple sequences alignment has been created. The scores between sequences also have been developed. We have constructed a phylogenetic tree and modified it with node and distance. Besides, we have generated sequence logos and ultimately developed the protein-protein interaction network. The small insulin signal transduction protein arrangement shows complex network between the functional proteins.

Stress induces remodelling of yeast interaction and co-expression networks

Abstract: Network analysis provides a powerful framework for the interpretation of genome-wide data. While static network approaches have proved fruitful, there is increasing interest in the insights gained from the analysis of cellular networks under different conditions. In this work, we study the effect of stress on cellular networks in fission yeast. Stress elicits a sophisticated and large scale cellular response, involving a shift of resources from cell growth and metabolism towards protection and maintenance. Previous work has suggested that these changes can be appreciated at the network level. In this paper, we study two types of cellular networks: gene co-regulation networks and weighted protein interaction networks. We show that in response to oxidative stress, the co-regulation networks re-organize towards a more modularised structure: while sets of genes become more tightly co-regulated, co-regulation between these modules is decreased. This shift translates into longer average shortest path length, increased transitivity, and decreased modular overlap in these networks. We also find a similar change in structure in the weighted protein interaction network in response to both oxidative stress and nitrogen starvation, confirming and extending previous findings. These changes in network structure could represent an increase in network robustness and/or the emergence of more specialised functional modules. Additionally, we find stress induces tighter co-regulation of non-coding RNAs, decreased functional importance of splicing factors, as well as changes in the centrality of genes involved in chromatin organization, cytoskeleton organization, cell division, and protein turnover.

Prediction of Protein Function Using Common-Neighbors in Protein-Protein Interaction Networks

Abstract: The recent high-throughput bio-techniques have provided us large-scale protein-protein interaction data through systematic identification of physical and genetic interactions among all proteins in an organism. Several previous studies have shown that using protein-protein interaction networks to predict protein function is a big step toward full understanding of the mechanisms of cells. However, the protein-protein interaction data derived from high-throughput experiments are typically very noisy, which presents great challenges to the existing methods. In this paper, we propose a novel common-neighbor-based model and a Bayesian framework to predict protein function on the basis of the small-world property of the protein-protein interaction network. We tested our approach on five data sets from various sources. The experimental results have shown that our approach has a better performance than several representative methods in terms of both precision and recall. In addition, our method is particularly effective to handle the high false-positive and false-negative rates in protein-protein interaction data