BACKGROUND Familial combined hyperlipidemia (FCHL) is the most commonly inherited hyperlipidemia in men. It constitutes a substantial risk factor for atherosclerosis patients. AIM To delineating the potential mechanism of FCHL by bioinformatics tools. MATERIALS AND METHODS In this study, Protein-Protein Interaction (PPI) network was constructed to identify the potential functional proteins ...

Understanding the evolution and structure of protein-protein interaction (PPI) networks is a central problem of systems biology. Since most processes in the cell are carried out by groups of proteins acting together, a theoretical model of how PPI networks develop based on duplications and mutations is an essential ingredient for understanding the complex wiring of the cell. Many different netw...

Detecting protein complexes is an important way to discover the relationship between network topological structure and its functional features in protein-protein interaction (PPI) network. The spectral clustering method is a popular approach. However, how to select its optimal Laplacian matrix is still an open problem. Here, we analyzed the performances of three graph Laplacian matrices (unnorm...

BACKGROUND Understanding protein complexes is important for understanding the science of cellular organization and function. Many computational methods have been developed to identify protein complexes from experimentally obtained protein-protein interaction (PPI) networks. However, interaction information obtained experimentally can be unreliable and incomplete. Reconstructing these PPI networ...

The protein-protein interaction (PPI) network offers a conceptual framework for better understanding the functional organization of the proteome. However, the intricacy of network complexity complicates comprehensive analysis. Here, we adopted a phylogenic grouping method combined with force-directed graph simulation to decompose the human PPI network in a multi-dimensional manner. This network...

MOTIVATION Networks have been used to model many real-world phenomena to better understand the phenomena and to guide experiments in order to predict their behavior. Since incorrect models lead to incorrect predictions, it is vital to have as accurate a model as possible. As a result, new techniques and models for analyzing and modeling real-world networks have recently been introduced. RESUL...

Modeling and analyzing protein-protein interaction (PPI) networks is an important problem in systems biology. Many random graph models were proposed to capture specific network properties or mimic the way real PPI networks might have evolved. In this paper we introduce a new generative model for PPI networks which is based on geometric random graphs and uses the whole connectivity information o...

Protein-protein interaction (PPI) networks are commonly explored for the identification of distinctive biological traits, such as pathways, modules, and functional motifs. In this respect, understanding the underlying network structure is vital to assess the significance of any discovered features. We recently demonstrated that PPI networks show degree-weighted behavior, whereby the probability...

The protein-protein interaction (PPI) network is crucial for cellular information processing and decision-making. With suitable inputs, PPI networks drive the cells to diverse functional outcomes such as cell proliferation or cell death. Here, we characterize the structural controllability of a large directed human PPI network comprising 6,339 proteins and 34,813 interactions. This network allo...

Proteins are essential macromolecules of life that carry out most cellular processes. Since proteins aggregate to perform function, and since protein-protein interaction (PPI) networks model these aggregations, one would expect to uncover new biology from PPI network topology. Hence, using PPI networks to predict protein function and role of protein pathways in disease has received attention. A...