Interaction network

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

Patterns and dynamics of users' behavior and interaction: Network analysis of an online community

Abstract: This research draws on longitudinal network data from an online community to examine patterns of users' behavior and social interaction, and infer the processes underpinning dynamics of system use. The online community represents a prototypical example of a complex evolving social network in which connections between users are established over time by online messages. We study the evolution of a variety of properties since the inception of the system, including how users create, reciprocate, and deepen relationships with one another, variations in users' gregariousness and popularity, reachability and typical distances among users, and the degree of local redundancy in the system. Results indicate that the system is a “small world” characterized by the emergence, in its early stages, of a hub-dominated structure with heterogeneity in users' behavior. We investigate whether hubs are responsible for holding the system together and facilitating information flow, examine first-mover advantages underpinning users' ability to rise to system prominence, and uncover gender differences in users' gregariousness, popularity, and local redundancy. We discuss the implications of the results for research on system use and evolving social networks, and for a host of applications, including information diffusion, communities of practice, and the security and robustness of information systems. © 2009 Wiley Periodicals, Inc.

Functional Proteomics Mapping of a Human Signaling Pathway

Abstract: Access to the human genome facilitates extensive functional proteomics studies. Here, we present an integrated approach combining large-scale protein interaction mapping, exploration of the interaction network, and cellular functional assays performed on newly identified proteins involved in a human signaling pathway. As a proof of principle, we studied the Smad signaling system, which is regulated by members of the transforming growth factor β (TGFβ) superfamily. We used two-hybrid screening to map Smad signaling protein–protein interactions and to establish a network of 755 interactions, involving 591 proteins, 179 of which were poorly or not annotated. The exploration of such complex interaction databases is improved by the use of PIMRider, a dedicated navigation tool accessible through the Web. The biological meaning of this network is illustrated by the presence of 18 known Smad-associated proteins. Functional assays performed in mammalian cells including siRNA knock-down experiments identified eight novel proteins involved in Smad signaling, thus validating this integrated functional proteomics approach.

Tissue specificity and the human protein interaction network.

Abstract: A protein interaction network describes a set of physical associations that can occur between proteins. However, within any particular cell or tissue only a subset of proteins is expressed and so only a subset of interactions can occur. Integrating interaction and expression data, we analyze here this interplay between protein expression and physical interactions in humans. Proteins only expressed in restricted cell types, like recently evolved proteins, make few physical interactions. Most tissue‐specific proteins do, however, bind to universally expressed proteins, and so can function by recruiting or modifying core cellular processes. Conversely, most ‘housekeeping’ proteins that are expressed in all cells also make highly tissue‐specific protein interactions. These results suggest a model for the evolution of tissue‐specific biology, and show that most, and possibly all, ‘housekeeping’ proteins actually have important tissue‐specific molecular interactions. Mol Syst Biol. 5: 260

Integrated network analysis platform for protein-protein interactions

Abstract: There is an increasing demand for network analysis of protein-protein interactions (PPIs). We introduce a web-based protein interaction network analysis platform (PINA), which integrates PPI data from six databases and provides network construction, filtering, analysis and visualization tools. We demonstrated the advantages of PINA by analyzing two human PPI networks; our results suggested a link between LKB1 and TGFbeta signaling, and revealed possible competitive interactors of p53 and c-Jun.

Analyzing and interpreting genome data at the network level with ConsensusPathDB.

Abstract: ConsensusPathDB consists of a comprehensive collection of human (as well as mouse and yeast) molecular interaction data integrated from 32 different public repositories and a web interface featuring a set of computational methods and visualization tools to explore these data. This protocol describes the use of ConsensusPathDB (http://consensuspathdb.org) with respect to the functional and network-based characterization of biomolecules (genes, proteins and metabolites) that are submitted to the system either as a priority list or together with associated experimental data such as RNA-seq. The tool reports interaction network modules, biochemical pathways and functional information that are significantly enriched by the user's input, applying computational methods for statistical over-representation, enrichment and graph analysis. The results of this protocol can be observed within a few minutes, even with genome-wide data. The resulting network associations can be used to interpret high-throughput data mechanistically, to characterize and prioritize biomarkers, to integrate different omics levels, to design follow-up functional assay experiments and to generate topology for kinetic models at different scales.