{"id":"https://openalex.org/W2162243457","doi":"https://doi.org/10.1093/bioinformatics/bti069","title":"Inferring pathways from gene lists using a literature-derived network of biological relationships","display_name":"Inferring pathways from gene lists using a literature-derived network of biological relationships","publication_year":2004,"publication_date":"2004-10-27","ids":{"openalex":"https://openalex.org/W2162243457","doi":"https://doi.org/10.1093/bioinformatics/bti069","mag":"2162243457","pmid":"https://pubmed.ncbi.nlm.nih.gov/15509611"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti069","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti069","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"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/A5003573457","display_name":"Dilip Rajagopalan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210114143","display_name":"GlaxoSmithKline (United States)","ror":"https://ror.org/025vn3989","country_code":"US","type":"company","lineage":["https://openalex.org/I188950975","https://openalex.org/I4210114143"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dilip Rajagopalan","raw_affiliation_strings":["Bioinformatics Sciences, GlaxoSmithKline Pharmaceuticals R&D 709 Swedeland Road, UW2230, King of Prussia, PA 19406\u22120939, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Sciences, GlaxoSmithKline Pharmaceuticals R&D 709 Swedeland Road, UW2230, King of Prussia, PA 19406\u22120939, USA","institution_ids":["https://openalex.org/I4210114143"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033246609","display_name":"Pankaj Agarwal","orcid":"https://orcid.org/0000-0002-4165-9990"},"institutions":[{"id":"https://openalex.org/I4210114143","display_name":"GlaxoSmithKline (United States)","ror":"https://ror.org/025vn3989","country_code":"US","type":"company","lineage":["https://openalex.org/I188950975","https://openalex.org/I4210114143"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pankaj Agarwal","raw_affiliation_strings":["Bioinformatics Sciences, GlaxoSmithKline Pharmaceuticals R&D 709 Swedeland Road, UW2230, King of Prussia, PA 19406\u22120939, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Sciences, GlaxoSmithKline Pharmaceuticals R&D 709 Swedeland Road, UW2230, King of Prussia, PA 19406\u22120939, USA","institution_ids":["https://openalex.org/I4210114143"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5003573457"],"corresponding_institution_ids":["https://openalex.org/I4210114143"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":1.3578,"has_fulltext":false,"cited_by_count":111,"citation_normalized_percentile":{"value":0.79253873,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"21","issue":"6","first_page":"788","last_page":"793"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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":0.9998000264167786,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9980000257492065,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9972000122070312,"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/subnetwork","display_name":"Subnetwork","score":0.7872341275215149},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.6862195730209351},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6152350306510925},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6057026982307434},{"id":"https://openalex.org/keywords/decipher","display_name":"DECIPHER","score":0.5650995373725891},{"id":"https://openalex.org/keywords/biological-pathway","display_name":"Biological pathway","score":0.5542115569114685},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.540653645992279},{"id":"https://openalex.org/keywords/heuristics","display_name":"Heuristics","score":0.5237576961517334},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5082871317863464},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4910552501678467},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.47567716240882874},{"id":"https://openalex.org/keywords/biological-database","display_name":"Biological database","score":0.4752521216869354},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4716036915779114},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.47069859504699707},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.4571523368358612},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.353284627199173},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2774972915649414},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21208426356315613}],"concepts":[{"id":"https://openalex.org/C2780186347","wikidata":"https://www.wikidata.org/wiki/Q11414","display_name":"Subnetwork","level":2,"score":0.7872341275215149},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.6862195730209351},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6152350306510925},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6057026982307434},{"id":"https://openalex.org/C164614171","wikidata":"https://www.wikidata.org/wiki/Q5204775","display_name":"DECIPHER","level":2,"score":0.5650995373725891},{"id":"https://openalex.org/C9927688","wikidata":"https://www.wikidata.org/wiki/Q4915012","display_name":"Biological pathway","level":4,"score":0.5542115569114685},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.540653645992279},{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.5237576961517334},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5082871317863464},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4910552501678467},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.47567716240882874},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.4752521216869354},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4716036915779114},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.47069859504699707},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.4571523368358612},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.353284627199173},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2774972915649414},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21208426356315613},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"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/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti069","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti069","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15509611","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15509611","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":"Evaluation Study"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1535641839","https://openalex.org/W2021239799","https://openalex.org/W2112811019","https://openalex.org/W2123106337","https://openalex.org/W2127938920","https://openalex.org/W2135000328","https://openalex.org/W2159203162","https://openalex.org/W2163480486","https://openalex.org/W2166898290","https://openalex.org/W4232903880","https://openalex.org/W4240689716","https://openalex.org/W7073816746"],"related_works":["https://openalex.org/W2564602748","https://openalex.org/W15348386","https://openalex.org/W4381571608","https://openalex.org/W2980263986","https://openalex.org/W2936116675","https://openalex.org/W2095724153","https://openalex.org/W2083623855","https://openalex.org/W2163262592","https://openalex.org/W2050326101","https://openalex.org/W2183784918"],"abstract_inverted_index":{"MOTIVATION:":[0],"A":[1,25],"number":[2,260],"of":[3,20,22,27,41,60,65,112,121,130,190,204,261,275],"omic":[4],"technologies":[5],"such":[6,47,141],"as":[7,88,94],"transcriptional":[8],"profiling,":[9],"proteomics,":[10],"literature":[11],"searches,":[12],"genetic":[13],"association,":[14],"etc.":[15],"help":[16,69],"in":[17,32,70,123],"the":[18,42,116,124,128,137,149,156,213,265,271,276],"identification":[19],"sets":[21],"important":[23],"genes.":[24],"subset":[26,120],"these":[28],"genes":[29,67,77,114,122,262],"may":[30,104],"act":[31],"a":[33,56,82,89,164,168,191,195,201,208,250,254,258],"coordinated":[34],"manner,":[35],"possibly":[36],"because":[37],"they":[38],"are":[39],"part":[40],"same":[43],"biological":[44,61,83,197,231,239],"pathway.":[45,266],"Interpreting":[46],"gene":[48],"lists":[49],"and":[50,91,167,178,234,236,273],"relating":[51],"them":[52,133],"to":[53,135,264],"pathways":[54],"is":[55,155,187],"challenging":[57],"task.":[58],"Databases":[59],"relationships":[62,75,131],"between":[63,76,97,132],"thousands":[64],"mammalian":[66],"can":[68,78,247],"deciphering":[71],"omics":[72,117],"data.":[73],"The":[74,119,184],"be":[79,106],"assembled":[80],"into":[81],"network":[84,103],"with":[85,127],"each":[86,92],"protein":[87],"node":[90],"relationship":[93],"an":[95,188],"edge":[96],"two":[98],"proteins":[99,147],"(or":[100],"nodes).":[101],"This":[102],"then":[105],"searched":[107],"for":[108,158,194],"subnetworks":[109,142],"consisting":[110],"largely":[111],"interesting":[113],"from":[115,148,181,253],"experiment.":[118,198],"subnetwork":[125],"along":[126],"web":[129],"helps":[134],"decipher":[136],"underlying":[138],"pathways.":[139,183],"Finding":[140],"that":[143,171,206,219,244],"maximally":[144],"include":[145],"all":[146],"query":[150,255],"set":[151,203],"but":[152],"few":[153],"others":[154],"focus":[157],"this":[159],"paper.":[160],"RESULTS:":[161],"We":[162,199,217,241],"present":[163],"heuristic":[165],"algorithm":[166],"scoring":[169,185],"function":[170,186],"work":[172],"well":[173],"both":[174],"on":[175,179,223],"simulated":[176,214],"data":[177,180],"known":[182],"extension":[189],"previous":[192],"study":[193],"single":[196],"use":[200],"simple":[202],"heuristics":[205],"provide":[207],"more":[209],"efficient":[210],"solution":[211],"than":[212],"annealing":[215],"method.":[216],"find":[218],"our":[220,245],"method":[221,246],"works":[222],"reasonably":[224],"complex":[225],"curated":[226],"networks":[227],"containing":[228],"approximately":[229,237],"9000":[230],"entities":[232],"(genes":[233],"metabolites),":[235],"30,000":[238],"relationships.":[240],"also":[242],"show":[243],"pick":[248],"up":[249],"pathway":[251],"signal":[252],"list":[256],"including":[257],"moderate":[259],"unrelated":[263],"In":[267],"addition,":[268],"we":[269],"quantify":[270],"sensitivity":[272],"specificity":[274],"technique.":[277]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":14},{"year":2012,"cited_by_count":9}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2016-06-24T00:00:00"}
