Nodes Having a Major Influence to Break Cooperation Define a Novel Centrality Measure: Game Centrality
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{"title"=>"Nodes Having a Major Influence to Break Cooperation Define a Novel Centrality Measure: Game Centrality", "type"=>"journal", "authors"=>[{"first_name"=>"Gabor I.", "last_name"=>"Simko", "scopus_author_id"=>"36441778300"}, {"first_name"=>"Peter", "last_name"=>"Csermely", "scopus_author_id"=>"8916910300"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "doi"=>"10.1371/journal.pone.0067159", "pui"=>"369209014", "sgr"=>"84879530007", "pmid"=>"23840611", "scopus"=>"2-s2.0-84879530007"}, "id"=>"f84893c9-9f00-3f87-b790-eb92897f0ba4", "abstract"=>"Cooperation played a significant role in the self-organization and evolution of living organisms. Both network topology and the initial position of cooperators heavily affect the cooperation of social dilemma games. We developed a novel simulation program package, called ‘NetworGame’, which is able to simulate any type of social dilemma games on any model, or real world networks with any assignment of initial cooperation or defection strategies to network nodes. The ability of initially defecting single nodes to break overall cooperation was called as ‘game centrality’. The efficiency of this measure was verified on well-known social networks, and was extended to ‘protein games’, i.e. the simulation of cooperation between proteins, or their amino acids. Hubs and in particular, party hubs of yeast protein-protein interaction networks had a large influence to convert the cooperation of other nodes to defection. Simulations on methionyl-tRNA synthetase protein structure network indicated an increased influence of nodes belonging to intra-protein signaling pathways on breaking cooperation. The efficiency of single, initially defecting nodes to convert the cooperation of other nodes to defection in social dilemma games may be an important measure to predict the importance of nodes in the integration and regulation of complex systems. Game centrality may help to design more efficient interventions to cellular networks (in forms of drugs), to ecosystems and social networks.", "link"=>"http://www.mendeley.com/research/nodes-having-major-influence-break-cooperation-define-novel-centrality-measure-game-centrality", "reader_count"=>30, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>5, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>13, "Student > Postgraduate"=>1, "Student > Master"=>3, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>5, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>13, "Student > Postgraduate"=>1, "Student > Master"=>3, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Engineering"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Mathematics"=>1, "Agricultural and Biological Sciences"=>3, "Medicine and Dentistry"=>3, "Business, Management and Accounting"=>3, "Physics and Astronomy"=>4, "Psychology"=>1, "Social Sciences"=>1, "Computer Science"=>6}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>4}, "Psychology"=>{"Psychology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>3}, "Computer Science"=>{"Computer Science"=>6}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Netherlands"=>1, "Hungary"=>1, "Japan"=>1, "Germany"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1106378"], "description"=>"<p>Prisoner’s dilemma game was simulated on a high-fidelity yeast interactome <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067159#pone.0067159-Ekman1\" target=\"_blank\">[36]</a>, and game centrality measures were calculated as described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067159#s4\" target=\"_blank\">Methods</a>. 171 proteins out of the 2,444 nodes of the high-fidelity yeast interactome were selected by selecting nodes, which diminished the cooperation level from ∼1 to 0.9 or below. Functional analysis of the 171 proteins was performed using the Cytoscape plug-in, BiNGO <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067159#pone.0067159-Maere1\" target=\"_blank\">[63]</a> to assess the over-representation of associated Gene Ontology molecular function terms. Gene Ontology Slim definitions for <i>Saccharomyces cerevisiae </i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067159#pone.0067159-TheGeneOntology1\" target=\"_blank\">[64]</a> were used discarding the evidence codes IEA (inferred from electronic annotation), ISS (inferred from sequence structural similarity) and NAS (non-traceable author statement). A hypergeometric test with false discovery rate correction <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067159#pone.0067159-Benjamini1\" target=\"_blank\">[65]</a> was used to select and visualize the significantly enriched GO functions at a level p<0.001, using the GO-s of the entire network as reference set. Colors represent functional categories: red, nucleus-related; blue, transport-related; green, signaling-related; yellow denotes other functions. The size of the circles represents the number of proteins found in the category.</p>", "links"=>[], "tags"=>["Computational biology", "Macromolecular structure analysis", "proteomics", "Protein interactions", "algorithms", "Computer modeling", "Applied mathematics", "game theory", "Sociology", "social networks", "yeast", "proteins", "having", "largest"], "article_id"=>735680, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Sociology"], "users"=>["Gabor I. Simko", "Peter Csermely"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0067159.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Functional_analysis_of_yeast_proteins_having_the_largest_game_centralities_/735680", "title"=>"Functional analysis of yeast proteins having the largest game centralities.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-28 04:24:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1106381"], "description"=>"a<p>Simulations of the prisoner’s dilemma game were performed as described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067159#s4\" target=\"_blank\">Methods</a> using the parameter set of (R = 3, T = 6, S = 0, P = 1). Correlation values between degree, betweenness centrality, GC in prisoner’s dilemma game, as well as phenotypic potential <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067159#pone.0067159-Levy1\" target=\"_blank\">[44]</a> were calculated for the 2,444 proteins of the high fidelity yeast interactome of Ekman <i>et al.</i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067159#pone.0067159-Ekman1\" target=\"_blank\">[36]</a>.</p>b<p>Data represent Goodman-Kruskal’s gamma values ± standard errors. Significance levels in parentheses were also calculated using Goodman-Kruskal’s gamma test (the null hypothesis being that the correlation is different from zero).</p>c<p>Using the R-package correlation test (<a href=\"http://personality-project.org/r/html/r.test.html\" target=\"_blank\">http://personality-project.org/r/html/r.test.html</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067159#pone.0067159-Steiger1\" target=\"_blank\">[62]</a>) the correlation between phenotypic potential and game centrality was significantly larger than the correlation between phenotypic potential and degree, or the correlation between phenotypic potential and betweenness centrality.</p>", "links"=>[], "tags"=>["Computational biology", "Macromolecular structure analysis", "proteomics", "Protein interactions", "algorithms", "Computer modeling", "Applied mathematics", "game theory", "Sociology", "social networks", "centrality", "betweenness", "phenotypic", "proteins", "fidelity", "yeast"], "article_id"=>735683, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Sociology"], "users"=>["Gabor I. Simko", "Peter Csermely"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0067159.t002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlations_of_game_centrality_GC_with_degree_betweenness_centrality_and_phenotypic_potential_of_proteins_in_a_high_fidelity_yeast_interactome_/735683", "title"=>"Correlations of game centrality (GC) with degree, betweenness centrality and phenotypic potential of proteins in a high fidelity yeast interactome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-06-28 04:24:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1106380"], "description"=>"a<p>Prisoner’s dilemma game was simulated using the high-fidelity yeast interactome of Ekman <i>et al.</i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067159#pone.0067159-Ekman1\" target=\"_blank\">[36]</a>, and game centrality measures were calculated as described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067159#s4\" target=\"_blank\">Methods</a>.</p>b<p>Initially all 2,444 nodes were cooperating except for 30 defecting nodes, which were randomly sampled 2000 times from 63 consensus party hubs (compiled as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067159#pone.0067159-Kovcs1\" target=\"_blank\">[43]</a>, see Table S1 of <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067159#pone.0067159.s001\" target=\"_blank\">Text S1</a>), from 145 consensus date hubs (compiled as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067159#pone.0067159-Kovcs1\" target=\"_blank\">[43]</a>, see Table S2 of <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067159#pone.0067159.s001\" target=\"_blank\">Text S1</a>), as well as from all the 2,444 nodes in the network.</p>c<p>Data represent sample means ± standard error. The distributions of the game centrality values were significantly different according to the chi-square test (χ<sup>2</sup>>400).</p>", "links"=>[], "tags"=>["Computational biology", "Macromolecular structure analysis", "proteomics", "Protein interactions", "algorithms", "Computer modeling", "Applied mathematics", "game theory", "Sociology", "social networks", "centrality", "hubs", "randomly", "nodes", "high-fidelity", "yeast", "protein-protein"], "article_id"=>735682, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Sociology"], "users"=>["Gabor I. Simko", "Peter Csermely"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0067159.t001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Game_centrality_of_party_hubs_date_hubs_and_randomly_selected_nodes_of_a_high_fidelity_yeast_protein_protein_interaction_network_/735682", "title"=>"Game centrality of party hubs, date hubs and randomly selected nodes of a high-fidelity yeast protein-protein interaction network.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-06-28 04:24:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1106383"], "description"=>"<div><p>Cooperation played a significant role in the self-organization and evolution of living organisms. Both network topology and the initial position of cooperators heavily affect the cooperation of social dilemma games. We developed a novel simulation program package, called ‘NetworGame’, which is able to simulate any type of social dilemma games on any model, or real world networks with any assignment of initial cooperation or defection strategies to network nodes. The ability of initially defecting single nodes to break overall cooperation was called as ‘game centrality’. The efficiency of this measure was verified on well-known social networks, and was extended to ‘protein games’, i.e. the simulation of cooperation between proteins, or their amino acids. Hubs and in particular, party hubs of yeast protein-protein interaction networks had a large influence to convert the cooperation of other nodes to defection. Simulations on methionyl-tRNA synthetase protein structure network indicated an increased influence of nodes belonging to intra-protein signaling pathways on breaking cooperation. The efficiency of single, initially defecting nodes to convert the cooperation of other nodes to defection in social dilemma games may be an important measure to predict the importance of nodes in the integration and regulation of complex systems. Game centrality may help to design more efficient interventions to cellular networks (in forms of drugs), to ecosystems and social networks.</p></div>", "links"=>[], "tags"=>["Computational biology", "Macromolecular structure analysis", "proteomics", "Protein interactions", "algorithms", "Computer modeling", "Applied mathematics", "game theory", "Sociology", "social networks", "having", "centrality"], "article_id"=>735685, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Sociology"], "users"=>["Gabor I. Simko", "Peter Csermely"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0067159", "stats"=>{"downloads"=>10, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nodes_Having_a_Major_Influence_to_Break_Cooperation_Define_a_Novel_Centrality_Measure_Game_Centrality_/735685", "title"=>"Nodes Having a Major Influence to Break Cooperation Define a Novel Centrality Measure: Game Centrality", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-06-28 04:24:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1106382"], "description"=>"a<p>Protein structure network of <i>E coli</i> methionyl-tRNA-synthetase was constructed, Prisoner’s dilemma game was simulated, and game centrality measures were calculated as described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067159#s4\" target=\"_blank\">Methods</a>.</p>b<p>Domains from top to bottom: the catalytic domain including the Rossmann-fold-1 (catalytic function), Rossmann-fold-2 and stem contact fold (KMSKS) sub-domains; the connecting peptide (CP) domain; the anticodon binding, carboxy-terminal domain, 43 signaling amino acids involved in the transmission of conformational change as shown by Ghosh and Vishveshwara <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067159#pone.0067159-Ghosh2\" target=\"_blank\">[46]</a>, whole methionyl-tRNA synthetase.</p>", "links"=>[], "tags"=>["Computational biology", "Macromolecular structure analysis", "proteomics", "Protein interactions", "algorithms", "Computer modeling", "Applied mathematics", "game theory", "Sociology", "social networks", "centrality", "methionyl-trna", "synthetase", "amino"], "article_id"=>735684, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Sociology"], "users"=>["Gabor I. Simko", "Peter Csermely"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0067159.t003", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Average_game_centrality_GC_values_for_E_coli_methionyl_tRNA_synthetase_amino_acids_/735684", "title"=>"Average game centrality (GC) values for <i>E. coli</i> methionyl-tRNA synthetase amino acids.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-06-28 04:24:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1106379"], "description"=>"<p>The protein structure network of <i>E. coli</i> methionyl-tRNA-synthetase was constructed, prisoner’s dilemma game was simulated, and game centrality measures were calculated as described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067159#s4\" target=\"_blank\">Methods</a>. Game centralities were overlaid to the 3D image of the protein and tRNA made by the PyMOL program package <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067159#pone.0067159-DeLano1\" target=\"_blank\">[66]</a>. tRNA<sup>Met</sup> is shown in green, the most influential amino acids spreading defection are marked red (these amino acids have the largest game centrality, GC values) and the least influential amino acids are blue (having the smallest GC values).</p>", "links"=>[], "tags"=>["Computational biology", "Macromolecular structure analysis", "proteomics", "Protein interactions", "algorithms", "Computer modeling", "Applied mathematics", "game theory", "Sociology", "social networks", "centralities", "methionyl-trna", "synthetase", "amino"], "article_id"=>735681, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Sociology"], "users"=>["Gabor I. Simko", "Peter Csermely"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0067159.g002", "stats"=>{"downloads"=>3, "page_views"=>31, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Game_centralities_of_E_coli_methionyl_tRNA_synthetase_amino_acids_/735681", "title"=>"Game centralities of <i>E.</i><i>coli</i> methionyl-tRNA synthetase amino acids.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-28 04:24:39"}

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Relative Metric

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