Hubs with Network Motifs Organize Modularity Dynamically in the Protein-Protein Interaction Network of Yeast
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{"title"=>"Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast", "type"=>"journal", "authors"=>[{"first_name"=>"Guangxu", "last_name"=>"Jin", "scopus_author_id"=>"7401563290"}, {"first_name"=>"Shihua", "last_name"=>"Zhang", "scopus_author_id"=>"35590912000"}, {"first_name"=>"Xiang Sun", "last_name"=>"Zhang", "scopus_author_id"=>"55961791600"}, {"first_name"=>"Luonan", "last_name"=>"Chen", "scopus_author_id"=>"26643448800"}], "year"=>2007, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-43149087837", "sgr"=>"43149087837", "pui"=>"351638149", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"18030341", "doi"=>"10.1371/journal.pone.0001207"}, "id"=>"fbc70fbe-46d2-346b-b7f5-d1dc89e2b9e4", "abstract"=>"BACKGROUND: It has been recognized that modular organization pervades biological complexity. Based on network analysis, 'party hubs' and 'date hubs' were proposed to understand the basic principle of module organization of biomolecular networks. However, recent study on hubs has suggested that there is no clear evidence for coexistence of 'party hubs' and 'date hubs'. Thus, an open question has been raised as to whether or not 'party hubs' and 'date hubs' truly exist in yeast interactome.\\n\\nMETHODOLOGY: In contrast to previous studies focusing on the partners of a hub or the individual proteins around the hub, our work aims to study the network motifs of a hub or interactions among individual proteins including the hub and its neighbors. Depending on the relationship between a hub's network motifs and protein complexes, we define two new types of hubs, 'motif party hubs' and 'motif date hubs', which have the same characteristics as the original 'party hubs' and 'date hubs' respectively. The network motifs of these two types of hubs display significantly different features in spatial distribution (or cellular localizations), co-expression in microarray data, controlling topological structure of network, and organizing modularity.\\n\\nCONCLUSION: By virtue of network motifs, we basically solved the open question about 'party hubs' and 'date hubs' which was raised by previous studies. Specifically, at the level of network motifs instead of individual proteins, we found two types of hubs, motif party hubs (mPHs) and motif date hubs (mDHs), whose network motifs display distinct characteristics on biological functions. In addition, in this paper we studied network motifs from a different viewpoint. That is, we show that a network motif should not be merely considered as an interaction pattern but be considered as an essential function unit in organizing modules of networks.", "link"=>"http://www.mendeley.com/research/hubs-network-motifs-organize-modularity-dynamically-proteinprotein-interaction-network-yeast", "reader_count"=>57, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>7, "Student > Doctoral Student"=>4, "Researcher"=>15, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>2, "Student > Master"=>4, "Student > Bachelor"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>7, "Student > Doctoral Student"=>4, "Researcher"=>15, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>2, "Student > Master"=>4, "Student > Bachelor"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>2}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>4, "Biochemistry, Genetics and Molecular Biology"=>7, "Mathematics"=>3, "Agricultural and Biological Sciences"=>31, "Medicine and Dentistry"=>3, "Business, Management and Accounting"=>1, "Computer Science"=>7}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>31}, "Computer Science"=>{"Computer Science"=>7}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Mathematics"=>{"Mathematics"=>3}, "Unspecified"=>{"Unspecified"=>4}}, "reader_count_by_country"=>{"United States"=>1, "Egypt"=>1, "Brazil"=>1, "United Kingdom"=>2, "Australia"=>1, "France"=>1, "Germany"=>1, "Spain"=>2}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/941125"], "description"=>"<p>The hub overlap of FYI and <i>HC<sup>fyi</sup></i> and the correctly divided mPHs and mDHs in the overlap.</p>", "links"=>[], "tags"=>["hub", "overlap", "fyi", "divided", "mphs", "mdhs"], "article_id"=>611536, "categories"=>["Medicine"], "users"=>["Guangxu Jin", "Shihua Zhang", "Xiang-Sun Zhang", "Luonan Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001207.g001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_hub_overlap_of_FYI_and_HC_fyi_and_the_correctly_divided_mPHs_and_mDHs_in_the_overlap_/611536", "title"=>"The hub overlap of FYI and <i>HC<sup>fyi</sup></i> and the correctly divided mPHs and mDHs in the overlap.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-11-21 00:25:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/941300"], "description"=>"<p>(A) The case of deleting mPHs and their motifs. In this case, the main components remain (the points in the same color are in the same component). (B) The case of deleting mDHs and their network motifs. Deleting the mDHs and their motif proteins causes the main components to disappear (the points in the same color are in the same component). (C) Deleting hubs one by one. The <i>HC<sup>fyi</sup></i> network is tolerant for the deletion of mPHs with their motifs. However, it is not tolerant for the deletion of mDHs with their motifs. (D) Deleting a randomly chosen set of 98 hubs with their motifs. We repeat the removal of 98 hubs with their motifs randomly for 1000 times. The sizes of the largest remaining components are all less than 555 that are the size of the largest component after removing the mPHs with their motifs. The sizes of the largest remaining components are all larger than 47 that are the size of the largest component after removing the mDHs with their motifs. Empirical P values are both less than 10<sup>−3</sup>. Biolayout <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001207#pone.0001207-Enright1\" target=\"_blank\">[53]</a> has been used to produce the figures in (A) and (B).</p>", "links"=>[], "tags"=>["mphs", "motifs", "mdhs"], "article_id"=>611721, "categories"=>["Medicine"], "users"=>["Guangxu Jin", "Shihua Zhang", "Xiang-Sun Zhang", "Luonan Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001207.g004", "stats"=>{"downloads"=>3, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Deleting_mPHs_with_their_motifs_and_mDHs_with_their_motifs_respectively_/611721", "title"=>"Deleting mPHs with their motifs and mDHs with their motifs respectively.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-11-21 00:28:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/941564"], "description"=>"<p>Sizes and Numbers of the network components after removal of mPHs and mDHs respectively</p>", "links"=>[], "tags"=>["numbers", "components", "mphs", "mdhs"], "article_id"=>611982, "categories"=>["Medicine"], "users"=>["Guangxu Jin", "Shihua Zhang", "Xiang-Sun Zhang", "Luonan Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001207.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sizes_and_Numbers_of_the_network_components_after_removal_of_mPHs_and_mDHs_respectively_/611982", "title"=>"Sizes and Numbers of the network components after removal of mPHs and mDHs respectively", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2007-11-21 00:33:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/941207"], "description"=>"<p>(A) Cellular localizations of mDHs. (B) Cellular localizations of mPHs.</p>", "links"=>[], "tags"=>["localizations", "mdhs"], "article_id"=>611632, "categories"=>["Medicine"], "users"=>["Guangxu Jin", "Shihua Zhang", "Xiang-Sun Zhang", "Luonan Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001207.g003", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_localizations_for_mDHs_and_mPHs_/611632", "title"=>"The localizations for mDHs and mPHs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-11-21 00:27:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/941532"], "description"=>"*<p>Mann-Whitney U test <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001207#pone.0001207-Bernard1\" target=\"_blank\">[54]</a>.</p>", "links"=>[], "tags"=>["differences", "samcs", "mdhs", "mphs", "microarray"], "article_id"=>611950, "categories"=>["Medicine"], "users"=>["Guangxu Jin", "Shihua Zhang", "Xiang-Sun Zhang", "Luonan Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001207.t003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Statistic_significance_for_the_differences_of_SAMCs_between_mDHs_and_mPHs_in_Microarray_data_/611950", "title"=>"Statistic significance for the differences of SAMCs between mDHs and mPHs in Microarray data", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2007-11-21 00:32:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/941366"], "description"=>"<p>In the middle of the panel, the red circles are abstract representations of pathways, where 14 smaller ones only connect with 6 mDHs (circles in light blue), and 26 larger ones connect with not only mDHs in blue circles (except the light blue one at the top of the panel) but also mPHs in orange circles. If more than one motif proteins of an mDH or an mPH are involved in one pathway, we connect the mDH or mPH with the pathway by an edge. Biolayout <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001207#pone.0001207-Enright1\" target=\"_blank\">[53]</a> has been used to produce the figure.</p>", "links"=>[], "tags"=>["motifs", "linking", "pathways", "mdhs"], "article_id"=>611786, "categories"=>["Medicine"], "users"=>["Guangxu Jin", "Shihua Zhang", "Xiang-Sun Zhang", "Luonan Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001207.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Network_motifs_linking_up_pathways_with_mDHs_and_mPHs_/611786", "title"=>"Network motifs linking up pathways with mDHs and mPHs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-11-21 00:29:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/941469"], "description"=>"<p>The proteins and interactions in <i>HC<sup>fyi</sup></i> and in all network motifs of <i>HC<sup>fyi</sup></i> respectively.</p>", "links"=>[], "tags"=>["proteins", "interactions", "motifs"], "article_id"=>611891, "categories"=>["Medicine"], "users"=>["Guangxu Jin", "Shihua Zhang", "Xiang-Sun Zhang", "Luonan Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001207.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_proteins_and_interactions_in_HC_fyi_and_in_all_network_motifs_of_HC_fyi_respectively_/611891", "title"=>"The proteins and interactions in <i>HC<sup>fyi</sup></i> and in all network motifs of <i>HC<sup>fyi</sup></i> respectively.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-11-21 00:31:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/463693", "https://ndownloader.figshare.com/files/463772", "https://ndownloader.figshare.com/files/463817", "https://ndownloader.figshare.com/files/463826", "https://ndownloader.figshare.com/files/463841"], "description"=>"<div><h3>Background</h3><p>It has been recognized that modular organization pervades biological complexity. Based on network analysis, ‘party hubs’ and ‘date hubs’ were proposed to understand the basic principle of module organization of biomolecular networks. However, recent study on hubs has suggested that there is no clear evidence for coexistence of ‘party hubs’ and ‘date hubs’. Thus, an open question has been raised as to whether or not ‘party hubs’ and ‘date hubs’ truly exist in yeast interactome.</p><h3>Methodology</h3><p>In contrast to previous studies focusing on the partners of a hub or the individual proteins around the hub, our work aims to study the network motifs of a hub or interactions among individual proteins including the hub and its neighbors. Depending on the relationship between a hub's network motifs and protein complexes, we define two new types of hubs, ‘motif party hubs’ and ‘motif date hubs’, which have the same characteristics as the original ‘party hubs’ and ‘date hubs’ respectively. The network motifs of these two types of hubs display significantly different features in spatial distribution (or cellular localizations), co-expression in microarray data, controlling topological structure of network, and organizing modularity.</p><h3>Conclusion</h3><p>By virtue of network motifs, we basically solved the open question about ‘party hubs’ and ‘date hubs’ which was raised by previous studies. Specifically, at the level of network motifs instead of individual proteins, we found two types of hubs, motif party hubs (mPHs) and motif date hubs (mDHs), whose network motifs display distinct characteristics on biological functions. In addition, in this paper we studied network motifs from a different viewpoint. That is, we show that a network motif should not be merely considered as an interaction pattern but be considered as an essential function unit in organizing modules of networks.</p></div>", "links"=>[], "tags"=>["hubs", "motifs", "modularity", "dynamically", "protein-protein", "yeast"], "article_id"=>151393, "categories"=>["Medicine"], "users"=>["Guangxu Jin", "Shihua Zhang", "Xiang-Sun Zhang", "Luonan Chen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0001207.s001", "https://dx.doi.org/10.1371/journal.pone.0001207.s002", "https://dx.doi.org/10.1371/journal.pone.0001207.s003", "https://dx.doi.org/10.1371/journal.pone.0001207.s004", "https://dx.doi.org/10.1371/journal.pone.0001207.s005"], "stats"=>{"downloads"=>17, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Hubs_with_Network_Motifs_Organize_Modularity_Dynamically_in_the_Protein_Protein_Interaction_Network_of_Yeast/151393", "title"=>"Hubs with Network Motifs Organize Modularity Dynamically in the Protein-Protein Interaction Network of Yeast", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2007-11-21 00:23:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/941502"], "description"=>"<p>There are totally 66 pathways in KEGG appearing in <i>HC<sup>fyi</sup></i> network.</p>", "links"=>[], "tags"=>["pathways"], "article_id"=>611922, "categories"=>["Medicine"], "users"=>["Guangxu Jin", "Shihua Zhang", "Xiang-Sun Zhang", "Luonan Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001207.t002", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Linking_with_signal_pathways_by_network_motifs_/611922", "title"=>"Linking with signal pathways by network motifs", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2007-11-21 00:32:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/941165"], "description"=>"<p>The spatial distribution of hubs.</p>", "links"=>[], "tags"=>["spatial"], "article_id"=>611593, "categories"=>["Medicine"], "users"=>["Guangxu Jin", "Shihua Zhang", "Xiang-Sun Zhang", "Luonan Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001207.g002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_spatial_distribution_of_hubs_/611593", "title"=>"The spatial distribution of hubs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-11-21 00:26:33"}

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Relative Metric

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