[PDF] Top 20 Topological transitions on protein-protein interaction networks
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Topological transitions on protein-protein interaction networks
... those topological transitions are consistent with real data of PPIN, we applied the same approach to data of Gene Co-expression Networks (GCN) of yeast freely available online from project Yeastnet ... See full document
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Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature.
... The protein names tagged by CPNM are normalized to their official symbols given in the Entrez Gene ...file) protein name mentions that we recognize in the PubMed abstract to their corresponding Entrez Gene ... See full document
13
Fault tolerance in protein interaction networks: stable bipartite subgraphs and redundant pathways.
... complex on the left (yellow nodes are in pathway 1 of BPM 541) from the other two (violet nodes are in pathway 2 of BPM 541), but because our search is limited to bipartite structure, our algorithm grouped both ... See full document
11
Protein Interaction Networks Reveal Novel Autism Risk Genes within GWAS Statistical Noise
... selected protein; and 3) the size of the largest connected component (LCC), the largest group of selected proteins that are reachable from each other in the ... See full document
11
An Algebro-topological description of protein domain structure.
... possible protein structures appears vast and continuous, and the relationship between primary, secondary and tertiary structure levels is ...complex. Protein structure comparison and classification is ... See full document
14
Exploring overlapping functional units with various structure in protein interaction networks.
... PPI networks resort to identifying cohesive protein complexes or functional modules [2–4] (Here, we do not distinguish protein complexes from functional modules because the underlying PPI ... See full document
11
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 ... See full document
17
Optimized null model for protein structure networks.
... observed networks [15] and to compare the behavior of certain topological properties ...other topological features not taken into account by the null model ...of protein structures have been ... See full document
9
Nodes with high centrality in protein interaction networks are responsible for driving signaling pathways in diabetic nephropathy
... The protein-protein interaction network for differentially expressed genes was constructed and ...Based on different parameters, 34 nodes were considered to have high centrality in this ...in ... See full document
11
Interface-resolved network of protein-protein interactions.
... between protein-protein interactions ...functional protein binding and thereby contains the detail necessary to describe the competition and cooperation between any pair of binding ...data on ... See full document
14
Unveiling protein functions through the dynamics of the interaction network.
... prediction on the information that can be directly extracted from the protein neighborhood, or statistically assessing a probability for a protein to be assigned to a given function, depending ... See full document
7
Identification of colorectal cancer related genes with mRMR and shortest path in protein-protein interaction network.
... based on (i) the gene expression profiles, and (ii) the shortest path analysis of functional protein association ...existing protein-protein interaction data from STRING (Search Tool ... See full document
12
Changes in protein interaction networks between normal and cancer conditions: Total chaos or ordered disorder?
... based on some static networks, but dynamic network based studies are needed to bring out more realistic ...interpretations. Protein interaction network with association of gene regulatory ... See full document
14
Sequence motifs in MADS transcription factors responsible for specificity and diversification of protein-protein interaction.
... how protein sequences define interaction specificity is largely missing, in particular for paralogous protein families with high sequence similarity, such as the plant MADS domain transcription ... See full document
13
Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria
... (based on at least a 20% homol- ogy) in the 74 differentially-expressed genes in Prochlorococcus ...regulatory networks are only hypothetical. Finally, we visualize the networks using the Cytoscape ... See full document
18
Dynamic circadian protein-protein interaction networks predict temporal organization of cellular functions
... depend on a variety of factors such as spatial restrains, restriction to specific tissues, relative protein abundance, mRNA processing, stoichiometry and interaction kinetics, complex formation and ... See full document
14
Identifying hubs in protein interaction networks.
... based on their neighbor coexpression character- ...LC networks. We note that both FYI and HC networks are constructed by combining literature-curated and high-throughput data so that the resulting ... See full document
10
Predicting Pharmacodynamic Drug-Drug Interactions through Signaling Propagation Interference on Protein-Protein Interaction Networks.
... Recently, the paradigm in drug discovery has shifted from single-target drugs to multi-target drugs [36]. Therefore, it becomes necessary to identify the performance of PD DDIs for multi- target drugs. To evaluate the ... See full document
13
Network compression as a quality measure for protein interaction networks.
... based on topology configuration was used to segregate random network models ...based on local vertex functionals for computing the entropy of chemical graphs and comparing chemical graphs [39], and another ... See full document
22
Identification of significant pathways in gastric cancer based on protein-protein interaction networks and cluster analysis
... ECM-receptor interaction (hsa04512) were all enriched in the two methods used to as- sess pathway ...Based on these findings, we sug- gest that the genes of the primary ... See full document
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