{"id":"https://openalex.org/W4221038323","doi":"https://doi.org/10.1093/bioinformatics/btac148","title":"Heterogeneous graph embedding model for predicting interactions between TF and target gene","display_name":"Heterogeneous graph embedding model for predicting interactions between TF and target gene","publication_year":2022,"publication_date":"2022-03-09","ids":{"openalex":"https://openalex.org/W4221038323","doi":"https://doi.org/10.1093/bioinformatics/btac148","pmid":"https://pubmed.ncbi.nlm.nih.gov/35266510"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac148","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac148","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/A5017713277","display_name":"Yu\u2010An Huang","orcid":"https://orcid.org/0000-0002-5346-2394"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yu-An Huang","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University , Shenzhen, China"],"raw_orcid":"https://orcid.org/0000-0002-5346-2394","affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University , Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063005114","display_name":"Gui-Qing Pan","orcid":null},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Gui-Qing Pan","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University , Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University , Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015805356","display_name":"Jia Wang","orcid":"https://orcid.org/0000-0001-5339-8954"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jia Wang","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University , Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University , Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100393871","display_name":"Jianqiang Li","orcid":"https://orcid.org/0000-0002-2208-962X"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian-Qiang Li","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University , Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University , Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047093288","display_name":"Jie Chen","orcid":"https://orcid.org/0000-0002-9811-1694"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jie Chen","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University , Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University , Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054130157","display_name":"Yang-Han Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang-Han Wu","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University , Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University , Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5015805356","https://openalex.org/A5017713277"],"corresponding_institution_ids":["https://openalex.org/I180726961"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.3358,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.52787751,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"38","issue":"9","first_page":"2554","last_page":"2560"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6758999824523926,"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":0.6758999824523926,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.16949999332427979,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.07460000365972519,"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":0.7453442215919495},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5305243730545044},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5197317600250244},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4749079942703247},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.46086323261260986},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4415937662124634},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.42344149947166443},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.41259878873825073},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3680141568183899},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1390584111213684},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.12857171893119812}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7453442215919495},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5305243730545044},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5197317600250244},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4749079942703247},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.46086323261260986},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4415937662124634},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.42344149947166443},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.41259878873825073},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3680141568183899},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1390584111213684},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.12857171893119812},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btac148","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac148","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:35266510","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35266510","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":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4000000059604645}],"awards":[{"id":"https://openalex.org/G2081278214","display_name":null,"funder_award_id":"2021A1515011153","funder_id":"https://openalex.org/F4320337111","funder_display_name":"Basic and Applied Basic Research Foundation of Guangdong Province"},{"id":"https://openalex.org/G3332848674","display_name":null,"funder_award_id":"R2020A045","funder_id":"https://openalex.org/F4320326705","funder_display_name":"Science, Technology and Innovation Commission of Shenzhen Municipality"},{"id":"https://openalex.org/G4784360784","display_name":null,"funder_award_id":"2020YFA0908700","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G7279309214","display_name":null,"funder_award_id":"62176164","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8318677017","display_name":null,"funder_award_id":"6197071246","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8594910186","display_name":null,"funder_award_id":"61806130","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320326705","display_name":"Science, Technology and Innovation Commission of Shenzhen Municipality","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320337111","display_name":"Basic and Applied Basic Research Foundation of Guangdong Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1990748933","https://openalex.org/W2026882865","https://openalex.org/W2032548898","https://openalex.org/W2076438782","https://openalex.org/W2102904139","https://openalex.org/W2104171413","https://openalex.org/W2104960492","https://openalex.org/W2129795133","https://openalex.org/W2139617657","https://openalex.org/W2155653793","https://openalex.org/W2166429927","https://openalex.org/W2171407623","https://openalex.org/W2737543579","https://openalex.org/W2782454362","https://openalex.org/W2786016794","https://openalex.org/W2896262061","https://openalex.org/W2896814836","https://openalex.org/W2974274234","https://openalex.org/W3080500495","https://openalex.org/W3113349968"],"related_works":["https://openalex.org/W2081900870","https://openalex.org/W3111219495","https://openalex.org/W2188500270","https://openalex.org/W2303858293","https://openalex.org/W2183306018","https://openalex.org/W2549990292","https://openalex.org/W2345479200","https://openalex.org/W2915512527","https://openalex.org/W51364034","https://openalex.org/W2951819827"],"abstract_inverted_index":{"MOTIVATION:":[0],"Identifying":[1],"the":[2,55,76,82,87,90,127,131,139,147,151,167,185,207],"target":[3,45,96],"genes":[4,41],"of":[5,10,89,130,153,169,173,189],"transcription":[6],"factors":[7],"(TFs)":[8],"is":[9,25,46,204,211],"great":[11],"significance":[12],"for":[13,38,42,49,114,215],"biomedical":[14],"researches.":[15],"However,":[16],"using":[17],"biological":[18],"experiments":[19],"to":[20,32,44,74],"identify":[21,75],"TF-target":[22,78,217],"gene":[23,79,97,218],"interactions":[24,219],"still":[26],"time":[27],"consuming,":[28],"expensive":[29],"and":[30,95,117,138,176,182,191,213,230],"limited":[31],"small":[33],"scale.":[34,223],"Existing":[35],"computational":[36],"methods":[37],"predicting":[39,216],"underlying":[40],"TF":[43,94],"mainly":[47],"proposed":[48,66,83,132,208],"their":[50,100],"binding":[51],"sites":[52],"rather":[53],"than":[54],"direct":[56],"interaction.":[57,80],"To":[58],"bridge":[59],"this":[60,64],"gap,":[61],"we":[62,162],"in":[63,102,120,157,184],"work":[65],"a":[67,121,135,179,221],"deep":[68],"learning":[69],"prediction":[70,109,128,168],"model,":[71],"named":[72],"HGETGI,":[73],"new":[77],"Specifically,":[81],"HGETGI":[84,209],"model":[85],"learns":[86],"patterns":[88],"known":[91],"interaction":[92],"between":[93],"complemented":[98],"with":[99],"involvement":[101],"different":[103],"human":[104],"disease":[105],"mechanisms.":[106],"It":[107,203],"performs":[108],"based":[110],"on":[111,134,166,220],"random":[112],"walk":[113],"meta-path":[115],"sampling":[116],"node":[118],"embedding":[119],"skip-gram":[122],"manner.":[123],"RESULTS:":[124],"We":[125],"evaluated":[126],"performance":[129],"method":[133,210],"real":[136],"dataset":[137,231],"experimental":[140],"results":[141],"show":[142],"that":[143,206],"it":[144],"can":[145],"achieve":[146],"average":[148],"area":[149],"under":[150],"curve":[152],"0.8519":[154],"\u00b1":[155],"0.0731":[156],"fivefold":[158],"cross":[159],"validation.":[160],"Besides,":[161],"conducted":[163],"case":[164],"studies":[165],"two":[170],"important":[171],"kinds":[172],"TF,":[174],"NFKB1":[175,190],"TP53.":[177],"As":[178],"result,":[180],"33":[181],"32":[183],"top-40":[186],"ranking":[187],"lists":[188],"TP53":[192],"were":[193],"successfully":[194],"confirmed":[195],"by":[196],"looking":[197],"up":[198],"another":[199],"public":[200],"database":[201],"(hTftarget).":[202],"envisioned":[205],"feasible":[212],"effective":[214],"large":[222],"AVAILABILITY":[224],"AND":[225],"IMPLEMENTATION:":[226],"The":[227],"source":[228],"code":[229],"are":[232,240],"available":[233,241],"at":[234,242],"https://github.com/PGTSING/HGETGI.":[235],"SUPPLEMENTARY":[236],"INFORMATION:":[237],"Supplementary":[238],"data":[239],"Bioinformatics":[243],"online.":[244]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}