Organization of Physical Interactomes as Uncovered by Network Schemas
Publication Date
October 24, 2008
Journal
PLOS Computational Biology
Authors
Eric Banks, Elena Nabieva, Bernard Chazelle & Mona Singh
Volume
4
Issue
10
Pages
e1000203
DOI
https://dx.plos.org/10.1371/journal.pcbi.1000203
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1000203
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/18949022
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2561054
Europe PMC
http://europepmc.org/abstract/MED/18949022
Web of Science
000261480700018
Scopus
55449101983
Mendeley
http://www.mendeley.com/research/organization-physical-interactomes-uncovered-network-schemas
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CiteULike | Further Information

Mendeley | Further Information

{"title"=>"Organization of physical interactomes as uncovered by network schemas", "type"=>"journal", "authors"=>[{"first_name"=>"Eric", "last_name"=>"Banks", "scopus_author_id"=>"57197332676"}, {"first_name"=>"Elena", "last_name"=>"Nabieva", "scopus_author_id"=>"10045123000"}, {"first_name"=>"Bernard", "last_name"=>"Chazelle", "scopus_author_id"=>"7005144537"}, {"first_name"=>"Mona", "last_name"=>"Singh", "scopus_author_id"=>"10042328600"}], "year"=>2008, "source"=>"PLoS Computational Biology", "identifiers"=>{"sgr"=>"55449101983", "doi"=>"10.1371/journal.pcbi.1000203", "issn"=>"1553734X", "pui"=>"352619807", "isbn"=>"1553-7358 (Electronic)\\r1553-734X (Linking)", "pmid"=>"18949022", "scopus"=>"2-s2.0-55449101983"}, "id"=>"2aeaacdc-e676-31cb-973c-d3248c23fa00", "abstract"=>"Large-scale protein-protein interaction networks provide new opportunities for understanding cellular organization and functioning. We introduce network schemas to elucidate shared mechanisms within interactomes. Network schemas specify descriptions of proteins and the topology of interactions among them. We develop algorithms for systematically uncovering recurring, over-represented schemas in physical interaction networks. We apply our methods to the S. cerevisiae interactome, focusing on schemas consisting of proteins described via sequence motifs and molecular function annotations and interacting with one another in one of four basic network topologies. We identify hundreds of recurring and over-represented network schemas of various complexity, and demonstrate via graph-theoretic representations how more complex schemas are organized in terms of their lower-order constituents. The uncovered schemas span a wide range of cellular activities, with many signaling and transport related higher-order schemas. We establish the functional importance of the schemas by showing that they correspond to functionally cohesive sets of proteins, are enriched in the frequency with which they have instances in the H. sapiens interactome, and are useful for predicting protein function. Our findings suggest that network schemas are a powerful paradigm for organizing, interrogating, and annotating cellular networks.", "link"=>"http://www.mendeley.com/research/organization-physical-interactomes-uncovered-network-schemas", "reader_count"=>50, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Researcher"=>18, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>1, "Student > Master"=>5, "Other"=>2, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Researcher"=>18, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>1, "Student > Master"=>5, "Other"=>2, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>3, "Mathematics"=>1, "Agricultural and Biological Sciences"=>34, "Medicine and Dentistry"=>1, "Neuroscience"=>1, "Computer Science"=>10}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>34}, "Computer Science"=>{"Computer Science"=>10}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Mathematics"=>{"Mathematics"=>1}}, "reader_count_by_country"=>{"United States"=>2, "United Kingdom"=>2, "Australia"=>2, "Switzerland"=>1, "Germany"=>1}, "group_count"=>3}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/454121", "https://ndownloader.figshare.com/files/454459", "https://ndownloader.figshare.com/files/454706", "https://ndownloader.figshare.com/files/454907", "https://ndownloader.figshare.com/files/455102", "https://ndownloader.figshare.com/files/455197", "https://ndownloader.figshare.com/files/455291", "https://ndownloader.figshare.com/files/455350", "https://ndownloader.figshare.com/files/455400", "https://ndownloader.figshare.com/files/455432", "https://ndownloader.figshare.com/files/455497", "https://ndownloader.figshare.com/files/455619", "https://ndownloader.figshare.com/files/455668", "https://ndownloader.figshare.com/files/455681", "https://ndownloader.figshare.com/files/455704", "https://ndownloader.figshare.com/files/455728"], "description"=>"<div><p>Large-scale protein-protein interaction networks provide new opportunities for understanding cellular organization and functioning. We introduce <em>network schemas</em> to elucidate shared mechanisms within interactomes. Network schemas specify descriptions of proteins and the topology of interactions among them. We develop algorithms for systematically uncovering recurring, over-represented schemas in physical interaction networks. We apply our methods to the <em>S. cerevisiae</em> interactome, focusing on schemas consisting of proteins described via sequence motifs and molecular function annotations and interacting with one another in one of four basic network topologies. We identify hundreds of recurring and over-represented network schemas of various complexity, and demonstrate via graph-theoretic representations how more complex schemas are organized in terms of their lower-order constituents. The uncovered schemas span a wide range of cellular activities, with many signaling and transport related higher-order schemas. We establish the functional importance of the schemas by showing that they correspond to functionally cohesive sets of proteins, are enriched in the frequency with which they have instances in the <em>H. sapiens</em> interactome, and are useful for predicting protein function. Our findings suggest that network schemas are a powerful paradigm for organizing, interrogating, and annotating cellular networks.</p></div>", "links"=>[], "tags"=>["interactomes", "uncovered", "schemas"], "article_id"=>149469, "categories"=>["Information And Computing Sciences", "Cancer", "Medicine"], "users"=>["Eric Banks", "Elena Nabieva", "Bernard Chazelle", "Mona Singh"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000203.s001", "https://dx.doi.org/10.1371/journal.pcbi.1000203.s002", "https://dx.doi.org/10.1371/journal.pcbi.1000203.s003", "https://dx.doi.org/10.1371/journal.pcbi.1000203.s004", "https://dx.doi.org/10.1371/journal.pcbi.1000203.s005", "https://dx.doi.org/10.1371/journal.pcbi.1000203.s006", "https://dx.doi.org/10.1371/journal.pcbi.1000203.s007", "https://dx.doi.org/10.1371/journal.pcbi.1000203.s008", "https://dx.doi.org/10.1371/journal.pcbi.1000203.s009", "https://dx.doi.org/10.1371/journal.pcbi.1000203.s010", "https://dx.doi.org/10.1371/journal.pcbi.1000203.s011", "https://dx.doi.org/10.1371/journal.pcbi.1000203.s012", "https://dx.doi.org/10.1371/journal.pcbi.1000203.s013", "https://dx.doi.org/10.1371/journal.pcbi.1000203.s014", "https://dx.doi.org/10.1371/journal.pcbi.1000203.s015", "https://dx.doi.org/10.1371/journal.pcbi.1000203.s016"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Organization_of_Physical_Interactomes_as_Uncovered_by_Network_Schemas/149469", "title"=>"Organization of Physical Interactomes as Uncovered by Network Schemas", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-10-24 02:37:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/917633"], "description"=>"<p>(A) An example of a triplet schema. Ras signaling involves a small G protein from the Ras family, which is regulated by a GTPase Activating Protein (GAP) and in turn regulates its effector kinase. The corresponding <i>GAP-Ras-Kinase</i> schema has a Ras protein interacting with a GAP protein as well as a kinase. (B) Instances of the <i>GAP-Ras-Kinase</i> schema in the <i>S. cerevisiae</i> physical interactome. Only a portion of the yeast physical protein-protein interaction network is shown. Ras family proteins are displayed as red octagons, GAP proteins as blue diamonds, and kinases as orange squares. Interactions that comprise an instance of a <i>GAP-Ras-Kinase</i> triplet schema are illustrated with thick solid lines, while other GAP-Ras and Ras-kinase interactions are marked by thick dashed lines. See <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000203#s4\" target=\"_blank\">Methods</a> for construction of physical interaction network and determination of protein annotations. This and subsequent figures are created using Cytoscape <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000203#pcbi.1000203-Shannon1\" target=\"_blank\">[74]</a>. (C) Schema topologies that are considered in this study.</p>", "links"=>[], "tags"=>["topologies"], "article_id"=>588086, "categories"=>["Information And Computing Sciences", "Infectious Diseases", "Medicine"], "users"=>["Eric Banks", "Elena Nabieva", "Bernard Chazelle", "Mona Singh"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000203.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Network_schemas_an_example_and_the_topologies_considered_/588086", "title"=>"Network schemas: an example and the topologies considered.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-10-24 02:14:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/917733"], "description"=>"<p>A pair of vertices connected by an edge corresponds to a pair schema. (A) Pfam emergent pair schemas, where each vertex is labeled with a Pfam motif. (B) Gene Ontology molecular function emergent pair schemas, where each vertex is labeled with a GO molecular function term, with the word “activity” dropped from term names. See also <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000203#pcbi.1000203.s005\" target=\"_blank\">Tables S1</a>, <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000203#pcbi.1000203.s006\" target=\"_blank\">S2</a> and <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000203#pcbi.1000203.s010\" target=\"_blank\">S6</a>.</p>", "links"=>[], "tags"=>["schemas", "uncovered"], "article_id"=>588195, "categories"=>["Information And Computing Sciences", "Infectious Diseases", "Medicine"], "users"=>["Eric Banks", "Elena Nabieva", "Bernard Chazelle", "Mona Singh"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000203.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Emergent_pair_schemas_uncovered_in_the_S_cerevisiae_interactome_/588195", "title"=>"Emergent pair schemas uncovered in the <i>S. cerevisiae</i> interactome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-10-24 02:16:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/917890"], "description"=>"<p>Pair schemas that are themselves emergent (<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000203#pcbi-1000203-g002\" target=\"_blank\">Figure 2</a>) are displayed as darker vertices. See also <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000203#pcbi.1000203.s007\" target=\"_blank\">Tables S3</a> and <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000203#pcbi.1000203.s008\" target=\"_blank\">S4</a>. (A) An illustration of the subgraph representation for triplet schemas. The triplet <i>MFS_1-DUP-AA_permease</i> (on the left) is mapped to two pair vertices, corresponding to the lower-order pair schemas making it up, connected by an edge. The edge is labeled in pink with the central motif of the triplet (DUP). (B) Pfam emergent triplet schemas. (C) An illustration of the triangle schema <i>DUP-AA_permease-Pfam-B_521</i>. The triangle <i>DUP-AA_permease-Pfam-B_521</i> is mapped to three pair vertices, corresponding to the lower-order pair schemas making it up, connected by edges; that is, it is represented as a triangle in the graph whose vertices represent pair schemas. The <i>DUP-Pfam-B_521</i> pair, colored pale in the pair-vertex graph, is not an emergent pair schema, whereas the other two pairs in the triangle, colored dark in the pair-vertex graph, are. (D) Pfam emergent triangle schemas.</p>", "links"=>[], "tags"=>["triplet", "triangle", "schemas", "uncovered", "represented", "graph", "vertices", "correspond"], "article_id"=>588339, "categories"=>["Information And Computing Sciences", "Infectious Diseases", "Medicine"], "users"=>["Eric Banks", "Elena Nabieva", "Bernard Chazelle", "Mona Singh"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000203.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Emergent_triplet_and_triangle_schemas_uncovered_in_the_S_cerevisiae_interactome_represented_in_a_graph_where_vertices_correspond_to_pair_schemas_/588339", "title"=>"Emergent triplet and triangle schemas uncovered in the <i>S. cerevisiae</i> interactome, represented in a graph where vertices correspond to pair schemas.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-10-24 02:18:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/918062"], "description"=>"<p>Triplet schemas that are themselves emergent (<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000203#pcbi-1000203-g003\" target=\"_blank\">Figure 3</a>) are displayed as darker vertices. (A) An illustration of the triplet subgraph representation of a Y-star schema. The Y-star (on the left) is mapped to three vertices corresponding to its lower-order triplet schemas, along with edges among them; that is, it is represented as a triangle in the graph whose vertices represent triplet schemas. The triplet subschemas of the Y-star are highlighted. The subschemas that are emergent triplets are highlighted in purple and represented as darker vertices. For ease of visualization, the central node of the Y-star is labeled in pink inside the triangle and connected to the vertices by dashed lines. (B) Pfam emergent Y-star schemas. See also <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000203#pcbi.1000203.s009\" target=\"_blank\">Table S5</a>.</p>", "links"=>[], "tags"=>["y-star", "schemas", "uncovered", "represented", "triangles", "graph", "vertex", "corresponds", "triplet"], "article_id"=>588508, "categories"=>["Information And Computing Sciences", "Infectious Diseases", "Medicine"], "users"=>["Eric Banks", "Elena Nabieva", "Bernard Chazelle", "Mona Singh"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000203.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Emergent_Y_star_schemas_uncovered_in_the_S_cerevisiae_interactome_represented_as_triangles_in_a_graph_where_each_vertex_corresponds_to_a_triplet_schema_/588508", "title"=>"Emergent Y-star schemas uncovered in the <i>S. cerevisiae</i> interactome, represented as triangles in a graph where each vertex corresponds to a triplet schema.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-10-24 02:21:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/918169"], "description"=>"<p>Schemas that are emergent in both organisms are displayed with red edges. Schemas that are emergent only in <i>H. sapiens</i> but that have instances in <i>S. cerevisiae</i> are shown with light blue edges. Schemas that are emergent only in <i>S. cerevisiae</i> but that have instances in <i>H. sapiens</i> are indicated with grey edges.</p>", "links"=>[], "tags"=>["schemas"], "article_id"=>588629, "categories"=>["Information And Computing Sciences", "Infectious Diseases", "Medicine"], "users"=>["Eric Banks", "Elena Nabieva", "Bernard Chazelle", "Mona Singh"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000203.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pfam_pair_schemas_that_are_found_in_both_H_sapiens_and_S_cerevisiae_/588629", "title"=>"Pfam pair schemas that are found in both <i>H. sapiens</i> and <i>S. cerevisiae</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-10-24 02:23:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/918308"], "description"=>"<p>Red vertices indicate Pfam motifs that are found in both organisms, and brown vertices indicate Pfam motifs found in <i>H. sapiens</i> but not <i>S. cerevisiae</i>.</p>", "links"=>[], "tags"=>["schemas", "emergent", "instances"], "article_id"=>588761, "categories"=>["Information And Computing Sciences", "Infectious Diseases", "Medicine"], "users"=>["Eric Banks", "Elena Nabieva", "Bernard Chazelle", "Mona Singh"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000203.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pfam_pair_schemas_that_are_emergent_in_H_sapiens_and_do_not_have_instances_in_the_S_cerevisiae_interactome_/588761", "title"=>"Pfam pair schemas that are emergent in <i>H. sapiens</i> and do not have instances in the <i>S. cerevisiae</i> interactome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-10-24 02:26:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/918444"], "description"=>"<p>Emergent <i>H. sapiens</i> pairs involving the <i>MAGE</i> family (A), and their instances (B).</p>", "links"=>[], "tags"=>["pairs", "involving", "instances"], "article_id"=>588901, "categories"=>["Information And Computing Sciences", "Infectious Diseases", "Medicine"], "users"=>["Eric Banks", "Elena Nabieva", "Bernard Chazelle", "Mona Singh"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000203.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Emergent_H_sapiens_pairs_involving_the_MAGE_family_A_and_their_instances_B_/588901", "title"=>"Emergent <i>H. sapiens</i> pairs involving the <i>MAGE</i> family (A), and their instances (B).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-10-24 02:28:21"}

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Relative Metric

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