{"id":"https://openalex.org/W4231872307","doi":"https://doi.org/10.4018/978-1-4666-1785-8.ch012","title":"Incorporating Network Topology Improves Prediction of Protein Interaction Networks from Transcriptomic Data","display_name":"Incorporating Network Topology Improves Prediction of Protein Interaction Networks from Transcriptomic Data","publication_year":2013,"publication_date":"2013-02-05","ids":{"openalex":"https://openalex.org/W4231872307","doi":"https://doi.org/10.4018/978-1-4666-1785-8.ch012"},"language":"en","primary_location":{"id":"doi:10.4018/978-1-4666-1785-8.ch012","doi":"https://doi.org/10.4018/978-1-4666-1785-8.ch012","is_oa":false,"landing_page_url":"https://doi.org/10.4018/978-1-4666-1785-8.ch012","pdf_url":null,"source":{"id":"https://openalex.org/S4306463409","display_name":"IGI Global eBooks","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/P4310320424","host_organization_name":"IGI Global","host_organization_lineage":["https://openalex.org/P4310320424"],"host_organization_lineage_names":["IGI Global"],"type":"ebook platform"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Knowledge Discovery for Bioinformatics Research","raw_type":"book-chapter"},"volume":{"id":"https://openalex.org/W2489733690","display_name":"Computational Knowledge Discovery for Bioinformatics Research"},"type":"book-chapter","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024204562","display_name":"Peter Emil Larsen","orcid":"https://orcid.org/0000-0001-6306-8289","observed_orcids":["https://orcid.org/0000-0001-6306-8289"]},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter E. Larsen","raw_affiliation_strings":["Argonne National Laboratory, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Argonne National Laboratory, USA","institution_ids":["https://openalex.org/I1282105669"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080700063","display_name":"F. Collart","orcid":"https://orcid.org/0000-0001-6942-4483","observed_orcids":["https://orcid.org/0000-0001-6942-4483"]},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Frank Collart","raw_affiliation_strings":["Argonne National Laboratory, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Argonne National Laboratory, USA","institution_ids":["https://openalex.org/I1282105669"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025440962","display_name":"Yang David Dai","orcid":"https://orcid.org/0000-0002-7638-849X","observed_orcids":["https://orcid.org/0000-0002-7638-849X"]},"institutions":[{"id":"https://openalex.org/I39422238","display_name":"University of Illinois Chicago","ror":"https://ror.org/02mpq6x41","country_code":"US","type":"education","lineage":["https://openalex.org/I39422238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yang Dai","raw_affiliation_strings":["University of Illinois at Chicago, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Illinois at Chicago, USA","institution_ids":["https://openalex.org/I39422238"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.39965558,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"203","last_page":"221"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10497","display_name":"Fungal and yeast genetics research","score":0.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-protein-interaction-network","display_name":"protein-protein interaction network","score":0.9539999961853027},{"id":"https://openalex.org/keywords/network-topology","display_name":"network topology","score":0.8140000104904175},{"id":"https://openalex.org/keywords/transcriptomic-data","display_name":"transcriptomic data","score":0.7139999866485596},{"id":"https://openalex.org/keywords/network-integration","display_name":"network integration","score":0.5580000281333923},{"id":"https://openalex.org/keywords/protein-protein-interaction-prediction","display_name":"protein-protein interaction prediction","score":0.5529999732971191}],"concepts":[{"id":"https://openalex.org/C9760119","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interactome","level":3,"score":0.8890312910079956},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.7051560878753662},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6189583539962769},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5852391123771667},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5729960203170776},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5380918383598328},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.46514996886253357},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.45674318075180054},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4282703101634979},{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.42021825909614563},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.4148993194103241},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4135608673095703},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26933369040489197},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17136415839195251},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10210034251213074},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.09696224331855774},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09303054213523865},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.4018/978-1-4666-1785-8.ch012","doi":"https://doi.org/10.4018/978-1-4666-1785-8.ch012","is_oa":false,"landing_page_url":"https://doi.org/10.4018/978-1-4666-1785-8.ch012","pdf_url":null,"source":{"id":"https://openalex.org/S4306463409","display_name":"IGI Global eBooks","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/P4310320424","host_organization_name":"IGI Global","host_organization_lineage":["https://openalex.org/P4310320424"],"host_organization_lineage_names":["IGI Global"],"type":"ebook platform"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Knowledge Discovery for Bioinformatics Research","raw_type":"book-chapter"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1588911128","https://openalex.org/W1989364985","https://openalex.org/W1992452843","https://openalex.org/W2001781153","https://openalex.org/W2061439657","https://openalex.org/W2079574756","https://openalex.org/W2093808519","https://openalex.org/W2112811019","https://openalex.org/W2116603180","https://openalex.org/W2118636185","https://openalex.org/W2145290999","https://openalex.org/W2149310258","https://openalex.org/W2163296115","https://openalex.org/W2171662214","https://openalex.org/W2172049947"],"related_works":["https://openalex.org/W1576401930","https://openalex.org/W2118169662","https://openalex.org/W3008844981","https://openalex.org/W2768035376","https://openalex.org/W159070292","https://openalex.org/W133025315","https://openalex.org/W4298031282","https://openalex.org/W2153161570","https://openalex.org/W2899065368","https://openalex.org/W1585902587"],"abstract_inverted_index":{"The":[0,76,101],"reconstruction":[1],"of":[2,13,60,68,96,103,110,116,127],"protein-protein":[3,62],"interaction":[4,121],"(PPI)":[5],"networks":[6,22,89,122],"from":[7],"high-throughput":[8],"experimental":[9,92],"data":[10,93],"is":[11],"one":[12],"the":[14,28,34,37,45,51,58,66,114],"most":[15],"challenging":[16],"problems":[17],"in":[18,44],"bioinformatics.":[19],"These":[20],"biological":[21,128],"have":[23],"specific":[24],"topologies":[25],"defined":[26],"by":[27],"functional":[29],"and":[30,36,73],"evolutionary":[31],"relationships":[32],"between":[33],"proteins":[35,42],"physical":[38],"limitations":[39],"imposed":[40],"on":[41,65],"interacting":[43],"three-dimensional":[46],"space.":[47],"In":[48],"this":[49,104],"paper,":[50],"authors":[52],"propose":[53],"a":[54,124],"novel":[55],"approach":[56],"for":[57],"identification":[59],"potential":[61],"interactions":[63],"based":[64],"integration":[67],"known":[69],"PPI":[70,88],"network":[71],"topology":[72,112],"transcriptomic":[74],"data.":[75],"proposed":[77],"method,":[78],"Function":[79],"Restricted":[80],"Value":[81],"Neighborhood":[82],"(FRV-N),":[83],"was":[84],"used":[85],"to":[86,119],"reconstruct":[87,120],"using":[90],"an":[91],"set":[94],"consisting":[95],"170":[97],"yeast":[98],"microarray":[99],"profiles.":[100],"results":[102],"analysis":[105,118],"demonstrate":[106],"that":[107],"incorporating":[108],"knowledge":[109],"interactome":[111],"improves":[113],"ability":[115],"transcriptome":[117],"with":[123],"high":[125],"degree":[126],"relevance.":[129]},"counts_by_year":[],"updated_date":"2026-10-10T09:11:00.788812","created_date":"2022-05-12T00:00:00"}