{"id":"https://openalex.org/W2885688533","doi":"https://doi.org/10.1093/bioinformatics/bty686","title":"KEDDY: a knowledge-based statistical gene set test method to detect differential functional protein\u2013protein interactions","display_name":"KEDDY: a knowledge-based statistical gene set test method to detect differential functional protein\u2013protein interactions","publication_year":2018,"publication_date":"2018-08-06","ids":{"openalex":"https://openalex.org/W2885688533","doi":"https://doi.org/10.1093/bioinformatics/bty686","mag":"2885688533","pmid":"https://pubmed.ncbi.nlm.nih.gov/30101275"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty686","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty686","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/A5101736401","display_name":"Sungwon Jung","orcid":"https://orcid.org/0000-0001-6002-554X"},"institutions":[{"id":"https://openalex.org/I12832649","display_name":"Gachon University","ror":"https://ror.org/03ryywt80","country_code":"KR","type":"education","lineage":["https://openalex.org/I12832649"]},{"id":"https://openalex.org/I4210088426","display_name":"Gachon University Gil Medical Center","ror":"https://ror.org/005nteb15","country_code":"KR","type":"healthcare","lineage":["https://openalex.org/I12832649","https://openalex.org/I4210088426"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Sungwon Jung","raw_affiliation_strings":["Department of Genome Medicine and Science, Gachon University College of Medicine, Incheon, Republic of Korea","Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Incheon, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genome Medicine and Science, Gachon University College of Medicine, Incheon, Republic of Korea","institution_ids":["https://openalex.org/I12832649"]},{"raw_affiliation_string":"Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Incheon, Republic of Korea","institution_ids":["https://openalex.org/I4210088426"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5101736401"],"corresponding_institution_ids":["https://openalex.org/I12832649","https://openalex.org/I4210088426"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.4963,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.6203895,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"35","issue":"4","first_page":"619","last_page":"627"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9534000158309937,"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":0.9534000158309937,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.019700000062584877,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.006300000008195639,"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/computer-science","display_name":"Computer science","score":0.6578291058540344},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6368852853775024},{"id":"https://openalex.org/keywords/differential","display_name":"Differential (mechanical device)","score":0.6173436641693115},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.568120539188385},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.434799462556839},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4224204123020172},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3630717396736145},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3419502377510071},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2399778962135315},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.14919039607048035},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1475180983543396}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6578291058540344},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6368852853775024},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.6173436641693115},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.568120539188385},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.434799462556839},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4224204123020172},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3630717396736145},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3419502377510071},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2399778962135315},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.14919039607048035},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1475180983543396},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bty686","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty686","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:30101275","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30101275","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":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W1516913835","https://openalex.org/W1908864745","https://openalex.org/W1965696861","https://openalex.org/W1965752870","https://openalex.org/W1982418865","https://openalex.org/W2016013112","https://openalex.org/W2037580712","https://openalex.org/W2051522090","https://openalex.org/W2054892633","https://openalex.org/W2067309281","https://openalex.org/W2095833325","https://openalex.org/W2108156593","https://openalex.org/W2109373478","https://openalex.org/W2110065044","https://openalex.org/W2110687686","https://openalex.org/W2111627808","https://openalex.org/W2112511512","https://openalex.org/W2112795434","https://openalex.org/W2114954827","https://openalex.org/W2116811581","https://openalex.org/W2121653135","https://openalex.org/W2124005900","https://openalex.org/W2124432707","https://openalex.org/W2130410032","https://openalex.org/W2132105963","https://openalex.org/W2136316164","https://openalex.org/W2136444502","https://openalex.org/W2139807849","https://openalex.org/W2145290999","https://openalex.org/W2146950091","https://openalex.org/W2146967305","https://openalex.org/W2147583496","https://openalex.org/W2149491227","https://openalex.org/W2151866902","https://openalex.org/W2158910699","https://openalex.org/W2159444728","https://openalex.org/W2161289668","https://openalex.org/W2224037795","https://openalex.org/W2465098683","https://openalex.org/W2556070101","https://openalex.org/W2607356028","https://openalex.org/W2915536738"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4224009465","https://openalex.org/W4306674287","https://openalex.org/W4286629047","https://openalex.org/W4205958290","https://openalex.org/W4384212932","https://openalex.org/W4390590544","https://openalex.org/W2096195258","https://openalex.org/W2990460313","https://openalex.org/W2973458857"],"abstract_inverted_index":{"MOTIVATION:":[0],"Identifying":[1],"differential":[2,29,46,72,96,166,188,194],"patterns":[3,30],"between":[4,14,81],"conditions":[5,83,109],"is":[6,67,222],"a":[7,57,68,77],"popular":[8],"approach":[9],"to":[10,41,51,177,192,225],"understanding":[11],"the":[12,112,149,198,208,211],"discrepancy":[13],"different":[15,33],"biological":[16],"contexts.":[17],"Although":[18],"many":[19],"statistical":[20,69],"tests":[21],"were":[22,39],"proposed":[23],"for":[24,71],"identifying":[25,162],"gene":[26,43,163,174,189,203,212],"sets":[27,44,164,180,190],"with":[28,45,84,132,165],"based":[31,119],"on":[32,95,120],"definitions":[34],"of":[35,59,62,76,79,98,103,115,210,220],"differentiality,":[36],"few":[37],"methods":[38,134,170],"suggested":[40],"identify":[42],"functional":[47,73,87,116,122],"protein":[48,74,117],"networks":[49,75,118],"due":[50],"computational":[52],"complexity.":[53],"RESULTS:":[54],"We":[55],"propose":[56],"method":[58,126,151],"Knowledge-based":[60],"Evaluation":[61],"Dependency":[63],"DifferentialitY":[64],"(KEDDY),":[65],"which":[66],"test":[70],"set":[78],"genes":[80,100],"two":[82,108],"utilizing":[85],"known":[86,121],"protein-protein":[88,123],"interaction":[89],"information.":[90],"Unlike":[91],"other":[92,169,193],"approaches":[93],"focused":[94],"expressions":[97],"individual":[99,104],"or":[101],"differentiality":[102,209],"interactions,":[105],"KEDDY":[106,139,183,221],"compares":[107],"by":[110],"evaluating":[111,171],"probability":[113],"distributions":[114],"interactions.":[124],"The":[125,217],"has":[127],"been":[128],"evaluated":[129],"and":[130,146,158,197],"compared":[131,191],"previous":[133,150],"through":[135],"simulation":[136],"studies,":[137],"where":[138],"achieves":[140],"significantly":[141],"improved":[142],"performance":[143,160],"in":[144,161,173],"accuracy":[145],"speed":[147],"than":[148,168],"that":[152,182,206],"does":[153],"not":[154],"use":[155],"prior":[156],"knowledge":[157],"better":[159],"interactions":[167],"changes":[172],"expressions.":[175],"Applications":[176],"cancer":[178,186],"data":[179,233],"show":[181],"identifies":[184],"alternative":[185],"subtype-related":[187],"expression-based":[195],"methods,":[196],"results":[199],"also":[200],"provide":[201],"detailed":[202],"regulatory":[204],"information":[205],"drives":[207],"sets.":[213],"AVAILABILITY":[214],"AND":[215],"IMPLEMENTATION:":[216],"Java":[218],"implementation":[219],"freely":[223],"available":[224,235],"non-commercial":[226],"users":[227],"at":[228,236],"https://sites.google.com/site/sjunggsm/keddy.":[229],"SUPPLEMENTARY":[230],"INFORMATION:":[231],"Supplementary":[232],"are":[234],"Bioinformatics":[237],"online.":[238]},"counts_by_year":[{"year":2020,"cited_by_count":6}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
