Interaction networks
Identifying hubs in protein interaction networks.
... large networks of protein-protein interactions has contributed to the identification of biochemical and signaling pathways, and to functional annotation of ...Such networks have been systematically ...
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Network compression as a quality measure for protein interaction networks.
... the networks to the systems they represent, then the relative compression rate should deteriorate with the addition of noise to ...interaction networks. Modularity is a hallmark of protein ...
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Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature.
... protein interaction relationship ...protein interaction networks and may be suitable to researchers in biology and biomedical field who wish to quickly study/explore protein networks specific ...
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Nodes with high centrality in protein interaction networks are responsible for driving signaling pathways in diabetic nephropathy
... protein-protein interaction network for differentially expressed genes was constructed and ...protein interaction networks tend to be present in pathways that co-occur in a biological ...
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Identification of significant pathways in gastric cancer based on protein-protein interaction networks and cluster analysis
... Gastric cancer is one of the most common and lethal cancers worldwide. However, despite its clinical importance, the regulatory mechanisms involved in the aggressiveness of this cancer are still poorly understood. A ...
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UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks
... UniHI 7 also stores gene expression in 19 different human tissue types derived from the Symatlas (40,41). Users can apply this data to highlight or exclude proteins (based on a chosen threshold level) to derive ...
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Predicting Pharmacodynamic Drug-Drug Interactions through Signaling Propagation Interference on Protein-Protein Interaction Networks.
... protein interaction networks, Human Protein Reference Database (HPRD) (9,117 proteins and 36,248 interactions), Interologous Interaction Database (I2D) (9,478 proteins and 43,593 interactions), and ...
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Module discovery by exhaustive search for densely connected, co-expressed regions in biomolecular interaction networks.
... In the most recent approach, Ulitsky and Shamir [29] compute connected subnetworks which, according to a statistical hypothesis test, are significantly co-expressed. Ulitsky and Shamir [29] also report that they ...
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Changes in protein interaction networks between normal and cancer conditions: Total chaos or ordered disorder?
... protein interaction networks (PINs) based on expression data of proteins involved in 10 major cancer signal transduction pathways were done in case of five different tissues ...protein-protein ...
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Fault tolerance in protein interaction networks: stable bipartite subgraphs and redundant pathways.
... protein interaction networks: whether there exist alternative pathways that can perform some required function if a gene essential to the main mechanism is defective, absent or ...physical ...
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Specificity and evolvability in eukaryotic protein interaction networks.
... In a recent review [34], Neduva and Russell postulated that linear motifs might act as ‘‘evolutionary interactions switches.’’ The authors claimed that, due to binding to a linear peptide stretch and due to the small ...
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Unraveling spurious properties of interaction networks with tailored random networks.
... of networks with predefined degree sequence (see, ...random networks (second ...random networks, we observed (in our simulation studies) dependencies between properties of networks and ...
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Dynamic circadian protein-protein interaction networks predict temporal organization of cellular functions
... interact with RORc) lengthened it. In addition, knocking down the androgen receptor (AR), which interestingly was found to interact with many proteins (including NONO, GSK3b, HDAC1, CREBBP, UBE2I and NCOR1/2), results ...
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The use of gene interaction networks to improve the identification of cancer driver genes
... Using threshold cut-off values genes are categorized as expressed or not. In Fig. 2, blue nodes partition of the bipartite graph represent mutated genes whilst nodes in red represent their expression status for different ...
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Construction and analysis of the protein-protein interaction networks based on gene expression profiles of Parkinson's disease.
... be involved in already known protein complexes associated with many biological processes. Out of the 37 markers, eight (CSNK2A1, CLTC, PARD3, IQGAP1, ACTB, ACTG1, CTNNA1 and GSN) were significantly involved in the core ...
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Exploring overlapping functional units with various structure in protein interaction networks.
... protein-protein interaction (PPI) networks are important for understanding cellular functional ...PPI networks show that the performance of RSRGM on detecting cohesive complexes and overlapping ...
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REDES DE INTERAÇÃO ENTRE AVES FRUGÍVORAS E PLANTAS: PADRÕES DE INTERAÇÃO E INFLUÊNCIA DE ATRIBUTOS
... species interaction networks, and these modules usually cluster functional similar ...the interaction networks formed by frugivorous birds and Miconia plants are modular and evaluated how ...
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Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria
... protein-protein interaction networks (Wallach et ...2014). Networks generated from these studies serve to identify potential targets for future biochemical and bioinformatics studies (Kaçar and ...
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Beta Diversity of Plant-Pollinator Networks and the Spatial Turnover of Pairwise Interactions
... plant-pollinator networks is well documented [21,28,37,38], the effect of flower abundance on the realization of pairwise interactions is hitherto poorly ...influence interaction patterns [24,39]. ...
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Structure-based network analysis of activation mechanisms in the ErbB family of receptor tyrosine kinases: the regulatory spine residues are global mediators of structural stability and allosteric interactions.
... the interaction networks to targeted perturbations of these residues that can abrogate their primary function and consequently lead to a significant loss of kinase ...structure networks in which ...
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