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{"title"=>"Linear Motif-Mediated Interactions Have Contributed to the Evolution of Modularity in Complex Protein Interaction Networks", "type"=>"journal", "authors"=>[{"first_name"=>"Inhae", "last_name"=>"Kim", "scopus_author_id"=>"55477736100"}, {"first_name"=>"Heetak", "last_name"=>"Lee", "scopus_author_id"=>"56397256200"}, {"first_name"=>"Seong Kyu", "last_name"=>"Han", "scopus_author_id"=>"56121169400"}, {"first_name"=>"Sanguk", "last_name"=>"Kim", "scopus_author_id"=>"7601602471"}], "year"=>2014, "source"=>"PLoS Computational Biology", "identifiers"=>{"sgr"=>"84908336844", "doi"=>"10.1371/journal.pcbi.1003881", "pui"=>"600311106", "issn"=>"15537358", "pmid"=>"25299147", "isbn"=>"2013018606", "scopus"=>"2-s2.0-84908336844"}, "id"=>"c231f67b-bae6-3f41-9e6b-04d76ae75f41", "abstract"=>"The modular architecture of protein-protein interaction (PPI) networks is evident in diverse species with a wide range of complexity. However, the molecular components that lead to the evolution of modularity in PPI networks have not been clearly identified. Here, we show that weak domain-linear motif interactions (DLIs) are more likely to connect different biological modules than strong domain-domain interactions (DDIs). This molecular division of labor is essential for the evolution of modularity in the complex PPI networks of diverse eukaryotic species. In particular, DLIs may compensate for the reduction in module boundaries that originate from increased connections between different modules in complex PPI networks. In addition, we show that the identification of biological modules can be greatly improved by including molecular characteristics of protein interactions. Our findings suggest that transient interactions have played a unique role in shaping the architecture and modularity of biological networks over the course of evolution.", "link"=>"http://www.mendeley.com/research/linear-motifmediated-interactions-contributed-evolution-modularity-complex-protein-interaction-netwo", "reader_count"=>50, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>14, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>14, "Student > Master"=>6, "Student > Bachelor"=>3, "Lecturer"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>14, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>14, "Student > Master"=>6, "Student > Bachelor"=>3, "Lecturer"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Biochemistry, Genetics and Molecular Biology"=>11, "Nursing and Health Professions"=>1, "Agricultural and Biological Sciences"=>23, "Medicine and Dentistry"=>3, "Arts and Humanities"=>1, "Business, Management and Accounting"=>1, "Computer Science"=>6}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>23}, "Computer Science"=>{"Computer Science"=>6}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>11}, "Unspecified"=>{"Unspecified"=>4}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Canada"=>3, "Argentina"=>1, "Korea (South)"=>1, "United States"=>1, "Brazil"=>1, "Slovenia"=>1, "India"=>1}, "group_count"=>2}

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• http://doi.org/10.1093/database/bav014
• http://doi.org/10.1038/srep26234
• http://doi.org/10.1002/prot.25646
• http://doi.org/10.3389/fmicb.2016.00530
• http://doi.org/10.1093/bioinformatics/btv522
• http://doi.org/10.1002/pro.2674

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/1710886"], "description"=>"<p>(<b>a</b>) DLI/DDI information improves the identification of biological modules. (<b>b</b>) Quality of modules identified using conventional PPI data vs. DLI/DDI data. Module quality reflects the similarity of biological annotations in protein pairs within modules. (<b>c</b>) A detail of the merge process for conventional PPI and DLI/DDI-identified modules. The two horizontal arrows represent the merge process for seven proteins associated with ‘Voltage-gated Na⁺/K⁺ channels’ and ‘Fcε signaling pathway’. Ordinal numbers of specific merge steps are shown.</p>", "links"=>[], "tags"=>["Complex Protein Interaction Networks", "modularity", "module", "species", "dli", "ddi", "evolution", "interaction", "PPI networks"], "article_id"=>1198718, "categories"=>["Uncategorised"], "users"=>["Inhae Kim", "Heetak Lee", "Seong Kyu Han", "Sanguk Kim"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003881.g006", "stats"=>{"downloads"=>0, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Employing_DLI_DDI_information_to_identify_biological_modules_/1198718", "title"=>"Employing DLI/DDI information to identify biological modules.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-09 02:52:59"}
• {"files"=>["https://ndownloader.figshare.com/files/1710883"], "description"=>"<p>(<b>a</b>) Odd ratio in functional groups. (<b>b</b>) Two functional groups, ‘cell-cell adhesion’ and ‘leukocyte migration’ were shown. (<b>c</b>) Odd ratio in protein complexes. (<b>d</b>) Two protein complexes, ‘RNA polymerase II’ and ‘BRCA1-associated genome surveillance’ were shown. (<b>e</b>) Odd ratio in subcellular localizations. (<b>f</b>) Two subcellular localizations, ‘cytoplasm’ and ‘nucleus’, were shown.</p>", "links"=>[], "tags"=>["Complex Protein Interaction Networks", "modularity", "module", "species", "dli", "ddi", "evolution", "interaction", "PPI networks"], "article_id"=>1198715, "categories"=>["Uncategorised"], "users"=>["Inhae Kim", "Heetak Lee", "Seong Kyu Han", "Sanguk Kim"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003881.g003", "stats"=>{"downloads"=>0, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enrichment_of_DLIs_and_DDIs_in_interactions_between_and_within_biological_modules_/1198715", "title"=>"Enrichment of DLIs and DDIs in interactions between and within biological modules.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-09 02:52:59"}
• {"files"=>["https://ndownloader.figshare.com/files/1710885"], "description"=>"<p>(<b>a</b>) Topological modularity, <i>M_PPI</i>, in nine representative eukaryotic species. (<b>b</b>) A schematic showing how increased complexity is associated with <i>M_PPI</i>. (<b>c</b>) Network modularity (<i>M_DLI/DDI</i>) in nine representative eukaryotic species. (<b>d</b>) A schematic showing how DLIs are associated with increased <i>M_DLI/DDI</i>. (<b>e</b>) The evolution of ‘cell-cell adhesion’ and ‘leukocyte migration’ groups is shown as an example.</p>", "links"=>[], "tags"=>["Complex Protein Interaction Networks", "modularity", "module", "species", "dli", "ddi", "evolution", "interaction", "PPI networks"], "article_id"=>1198717, "categories"=>["Uncategorised"], "users"=>["Inhae Kim", "Heetak Lee", "Seong Kyu Han", "Sanguk Kim"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003881.g005", "stats"=>{"downloads"=>0, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_expansion_of_DLIs_contributed_to_the_increase_in_modularity_of_metazoan_PPI_networks_/1198717", "title"=>"The expansion of DLIs contributed to the increase in modularity of metazoan PPI networks.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-09 02:52:59"}
• {"files"=>["https://ndownloader.figshare.com/files/1710884"], "description"=>"<p>(<b>a</b>) The number of conserved DLIs and DDIs in eukaryotic species. Values for nine representative eukaryotic species are shown. (<b>b</b>) Average proportion of DLIs and DDIs in 45 nonmetazoan and 54 metazoan species.</p>", "links"=>[], "tags"=>["Complex Protein Interaction Networks", "modularity", "module", "species", "dli", "ddi", "evolution", "interaction", "PPI networks"], "article_id"=>1198716, "categories"=>["Uncategorised"], "users"=>["Inhae Kim", "Heetak Lee", "Seong Kyu Han", "Sanguk Kim"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003881.g004", "stats"=>{"downloads"=>0, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expansion_of_DLIs_in_metazoan_PPI_networks_/1198716", "title"=>"Expansion of DLIs in metazoan PPI networks.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-09 02:52:59"}
• {"files"=>["https://ndownloader.figshare.com/files/1710881"], "description"=>"<p>(<b>a</b>) Categorizing human PPIs as DDIs or DLIs. A part of the human PPI network is shown to visualize DDI/DLI-assigned network. (<b>b</b>) Quality assessment of linear motifs during classification process. (<b>c</b>) Comparison of DDIs and DLIs categorized using our method to reference sets. (<b>d</b>) Edge clustering coefficients of DDIs and DLIs in the human PPI network. Grey bars show the distribution of average edge clustering coefficients in 10⁵ networks with randomly assigned DDIs and DLIs.</p>", "links"=>[], "tags"=>["Complex Protein Interaction Networks", "modularity", "module", "species", "dli", "ddi", "evolution", "interaction", "PPI networks"], "article_id"=>1198713, "categories"=>["Uncategorised"], "users"=>["Inhae Kim", "Heetak Lee", "Seong Kyu Han", "Sanguk Kim"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003881.g002", "stats"=>{"downloads"=>0, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_DDI_and_DLI_assigned_human_PPI_network_/1198713", "title"=>"DDI and DLI-assigned human PPI network.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-09 02:52:59"}
• {"files"=>["https://ndownloader.figshare.com/files/1710880"], "description"=>"<p>(<b>a</b>) The relationship between tie strength and community structure is well established in social networks. (<b>b</b>) DDIs and DLIs correspond to strong and weak interactions in PPI networks, respectively.</p>", "links"=>[], "tags"=>["Complex Protein Interaction Networks", "modularity", "module", "species", "dli", "ddi", "evolution", "interaction", "PPI networks"], "article_id"=>1198712, "categories"=>["Uncategorised"], "users"=>["Inhae Kim", "Heetak Lee", "Seong Kyu Han", "Sanguk Kim"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003881.g001", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Interaction_strength_and_modular_architecture_in_networks_/1198712", "title"=>"Interaction strength and modular architecture in networks.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-09 02:52:59"}
• {"files"=>["https://ndownloader.figshare.com/files/1710887", "https://ndownloader.figshare.com/files/1710888", "https://ndownloader.figshare.com/files/1710889", "https://ndownloader.figshare.com/files/1710890", "https://ndownloader.figshare.com/files/1710891", "https://ndownloader.figshare.com/files/1710892", "https://ndownloader.figshare.com/files/1710893", "https://ndownloader.figshare.com/files/1710894", "https://ndownloader.figshare.com/files/1710895", "https://ndownloader.figshare.com/files/1710896", "https://ndownloader.figshare.com/files/1710897", "https://ndownloader.figshare.com/files/1710898", "https://ndownloader.figshare.com/files/1710899", "https://ndownloader.figshare.com/files/1710900", "https://ndownloader.figshare.com/files/1710901", "https://ndownloader.figshare.com/files/1710902", "https://ndownloader.figshare.com/files/1710903", "https://ndownloader.figshare.com/files/1710904", "https://ndownloader.figshare.com/files/1710905"], "description"=>"<div><p>The modular architecture of protein-protein interaction (PPI) networks is evident in diverse species with a wide range of complexity. However, the molecular components that lead to the evolution of modularity in PPI networks have not been clearly identified. Here, we show that weak domain-linear motif interactions (DLIs) are more likely to connect different biological modules than strong domain-domain interactions (DDIs). This molecular division of labor is essential for the evolution of modularity in the complex PPI networks of diverse eukaryotic species. In particular, DLIs may compensate for the reduction in module boundaries that originate from increased connections between different modules in complex PPI networks. In addition, we show that the identification of biological modules can be greatly improved by including molecular characteristics of protein interactions. Our findings suggest that transient interactions have played a unique role in shaping the architecture and modularity of biological networks over the course of evolution.</p></div>", "links"=>[], "tags"=>["Complex Protein Interaction Networks", "modularity", "module", "species", "dli", "ddi", "evolution", "interaction", "PPI networks"], "article_id"=>1198719, "categories"=>["Uncategorised"], "users"=>["Inhae Kim", "Heetak Lee", "Seong Kyu Han", "Sanguk Kim"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1003881.s001", "https://dx.doi.org/10.1371/journal.pcbi.1003881.s002", "https://dx.doi.org/10.1371/journal.pcbi.1003881.s003", "https://dx.doi.org/10.1371/journal.pcbi.1003881.s004", "https://dx.doi.org/10.1371/journal.pcbi.1003881.s005", "https://dx.doi.org/10.1371/journal.pcbi.1003881.s006", "https://dx.doi.org/10.1371/journal.pcbi.1003881.s007", "https://dx.doi.org/10.1371/journal.pcbi.1003881.s008", "https://dx.doi.org/10.1371/journal.pcbi.1003881.s009", "https://dx.doi.org/10.1371/journal.pcbi.1003881.s010", "https://dx.doi.org/10.1371/journal.pcbi.1003881.s011", "https://dx.doi.org/10.1371/journal.pcbi.1003881.s012", "https://dx.doi.org/10.1371/journal.pcbi.1003881.s013", "https://dx.doi.org/10.1371/journal.pcbi.1003881.s014", "https://dx.doi.org/10.1371/journal.pcbi.1003881.s015", "https://dx.doi.org/10.1371/journal.pcbi.1003881.s016", "https://dx.doi.org/10.1371/journal.pcbi.1003881.s017", "https://dx.doi.org/10.1371/journal.pcbi.1003881.s018", "https://dx.doi.org/10.1371/journal.pcbi.1003881.s019"], "stats"=>{"downloads"=>20, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Linear_Motif_Mediated_Interactions_Have_Contributed_to_the_Evolution_of_Modularity_in_Complex_Protein_Interaction_Networks_/1198719", "title"=>"Linear Motif-Mediated Interactions Have Contributed to the Evolution of Modularity in Complex Protein Interaction Networks", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-10-09 02:52:59"}

PMC Usage Stats | Further Information

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F1000Prime | Further Information

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• {"year"=>2017, "month"=>8, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2017-08-28T08:41:14Z"}
• {"year"=>2017, "month"=>9, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2017-09-25T08:41:19Z"}
• {"year"=>2017, "month"=>10, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2017-10-30T08:41:39Z"}
• {"year"=>2017, "month"=>11, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2017-11-27T09:41:20Z"}
• {"year"=>2017, "month"=>12, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2017-12-25T09:41:14Z"}
• {"year"=>2018, "month"=>1, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2018-01-29T09:40:56Z"}
• {"year"=>2018, "month"=>2, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2018-02-26T09:40:59Z"}
• {"year"=>2018, "month"=>3, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2018-03-26T08:41:01Z"}
• {"year"=>2018, "month"=>4, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2018-04-30T08:40:57Z"}
• {"year"=>2018, "month"=>5, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2018-05-28T08:40:59Z"}
• {"year"=>2018, "month"=>6, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2018-06-25T08:40:59Z"}
• {"year"=>2018, "month"=>7, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2018-07-30T08:41:07Z"}
• {"year"=>2018, "month"=>8, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2018-08-27T08:41:22Z"}
• {"year"=>2018, "month"=>9, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2018-09-24T08:41:09Z"}
• {"year"=>2018, "month"=>10, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2018-10-29T08:41:11Z"}
• {"year"=>2018, "month"=>11, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2018-11-26T09:41:14Z"}
• {"year"=>2018, "month"=>12, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2018-12-31T09:41:22Z"}
• {"year"=>2019, "month"=>1, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2019-01-28T09:41:09Z"}
• {"year"=>2019, "month"=>2, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2019-02-25T09:41:07Z"}
• {"year"=>2019, "month"=>3, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2019-03-25T08:41:02Z"}
• {"year"=>2019, "month"=>4, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2019-04-29T08:41:11Z"}
• {"year"=>2019, "month"=>5, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2019-05-27T08:41:23Z"}
• {"year"=>2019, "month"=>6, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2019-06-24T08:41:10Z"}
• {"year"=>2019, "month"=>7, "doi"=>"10.1371/journal.pcbi.1003881", "f1000_id"=>"720591107", "url"=>"https://f1000.com/prime/720591107", "score"=>3, "classifications"=>["new_finding"], "updated_at"=>"2019-07-15T08:41:22Z"}