{"id":"https://openalex.org/W4210572475","doi":"https://doi.org/10.1109/tcbb.2022.3145796","title":"Constructing a Cancer Patient-Specific Network Based on Second-Order Partial Correlations of Gene Expression and DNA Methylation","display_name":"Constructing a Cancer Patient-Specific Network Based on Second-Order Partial Correlations of Gene Expression and DNA Methylation","publication_year":2022,"publication_date":"2022-01-25","ids":{"openalex":"https://openalex.org/W4210572475","doi":"https://doi.org/10.1109/tcbb.2022.3145796","pmid":"https://pubmed.ncbi.nlm.nih.gov/35077366"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2022.3145796","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3145796","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5103167446","display_name":"Wook Lee","orcid":"https://orcid.org/0000-0001-5280-4244"},"institutions":[{"id":"https://openalex.org/I191879574","display_name":"Inha University","ror":"https://ror.org/01easw929","country_code":"KR","type":"education","lineage":["https://openalex.org/I191879574"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Wook Lee","raw_affiliation_strings":["Department of Computer Engineering, Inha University, Incheon, South Korea"],"raw_orcid":"https://orcid.org/0000-0001-5280-4244","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Inha University, Incheon, South Korea","institution_ids":["https://openalex.org/I191879574"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101494954","display_name":"Seokwoo Lee","orcid":"https://orcid.org/0000-0001-7545-6334"},"institutions":[{"id":"https://openalex.org/I191879574","display_name":"Inha University","ror":"https://ror.org/01easw929","country_code":"KR","type":"education","lineage":["https://openalex.org/I191879574"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Seokwoo Lee","raw_affiliation_strings":["Department of Computer Engineering, Inha University, Incheon, South Korea"],"raw_orcid":"https://orcid.org/0000-0001-7545-6334","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Inha University, Incheon, South Korea","institution_ids":["https://openalex.org/I191879574"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073616869","display_name":"Kyungsook Han","orcid":"https://orcid.org/0000-0001-9900-6741"},"institutions":[{"id":"https://openalex.org/I191879574","display_name":"Inha University","ror":"https://ror.org/01easw929","country_code":"KR","type":"education","lineage":["https://openalex.org/I191879574"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Kyungsook Han","raw_affiliation_strings":["Department of Computer Engineering, Inha University, Incheon, South Korea"],"raw_orcid":"https://orcid.org/0000-0001-9900-6741","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Inha University, Incheon, South Korea","institution_ids":["https://openalex.org/I191879574"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I191879574"],"apc_list":null,"apc_paid":null,"fwci":0.1733,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.45968981,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"20","issue":"1","first_page":"266","last_page":"276"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9994000196456909,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.9933000206947327,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.7648866176605225},{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.7193949818611145},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6025392413139343},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5617719888687134},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.5491552352905273},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5436081886291504},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.523016631603241},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.49950218200683594},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.48963218927383423},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.44782203435897827},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4424092173576355},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.4131099283695221},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3283287584781647}],"concepts":[{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.7648866176605225},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.7193949818611145},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6025392413139343},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5617719888687134},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.5491552352905273},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5436081886291504},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.523016631603241},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.49950218200683594},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.48963218927383423},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.44782203435897827},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4424092173576355},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4131099283695221},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3283287584781647}],"mesh":[{"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":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"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":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2022.3145796","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3145796","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35077366","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35077366","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.5099999904632568,"id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G940708036","display_name":null,"funder_award_id":"2020R1A2B5B01096299","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"}],"funders":[{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W1966327575","https://openalex.org/W1999574084","https://openalex.org/W2006255103","https://openalex.org/W2018680913","https://openalex.org/W2025183726","https://openalex.org/W2039104072","https://openalex.org/W2058951658","https://openalex.org/W2110065044","https://openalex.org/W2134061119","https://openalex.org/W2150000105","https://openalex.org/W2158217645","https://openalex.org/W2168775836","https://openalex.org/W2508622936","https://openalex.org/W2558586574","https://openalex.org/W2948505931","https://openalex.org/W2969272216","https://openalex.org/W2994725382","https://openalex.org/W2995630912","https://openalex.org/W2999309192","https://openalex.org/W3014459671","https://openalex.org/W3027224324","https://openalex.org/W3038114454","https://openalex.org/W3041047318","https://openalex.org/W3076814102","https://openalex.org/W3082700550","https://openalex.org/W4235169531"],"related_works":["https://openalex.org/W2214376880","https://openalex.org/W3212149434","https://openalex.org/W2073893804","https://openalex.org/W2291484187","https://openalex.org/W2902329290","https://openalex.org/W2139872319","https://openalex.org/W2052355316","https://openalex.org/W2046964473","https://openalex.org/W2107880877","https://openalex.org/W2151182744"],"abstract_inverted_index":{"Typically":[0],"patient-specific":[1,67,82,122,172],"gene":[2,7,16,31,44,68,73,90,145,151,173],"networks":[3,12,123,130,156],"are":[4,131],"constructed":[5,120],"with":[6],"expression":[8,45,74,91],"data":[9],"only.":[10],"Such":[11],"cannot":[13],"distinguish":[14],"direct":[15,105],"interactions":[17,20,106],"from":[18,84,154],"indirect":[19],"via":[21],"others":[22],"such":[23,51],"as":[24,52],"the":[25,99,111,155,161],"effect":[26,112],"of":[27,38,89,113,127,138,164,178],"epigenetic":[28,49],"events":[29,50],"to":[30],"activity.":[32],"There":[33],"is":[34],"an":[35],"increasing":[36],"evidence":[37],"inter-individual":[39],"variations":[40],"not":[41],"only":[42],"in":[43,48,134,141,159],"but":[46],"also":[47],"DNA":[53,76,93,114],"methylation.":[54,115],"In":[55,147],"this":[56,117],"paper":[57],"we":[58,119],"propose":[59],"a":[60,65,81],"new":[61],"method":[62],"for":[63,124],"constructing":[64],"cancer":[66,139,165,179],"correlation":[69],"network":[70,83,103],"using":[71],"both":[72],"and":[75,92,98,140,175],"methylation":[77,94],"data.":[78],"We":[79],"derive":[80],"differential":[85],"second-order":[86],"partial":[87],"correlations":[88,174],"between":[95,107],"normal":[96],"samples":[97],"patient":[100],"sample.":[101],"The":[102,129],"represents":[104],"genes":[108],"by":[109],"controlling":[110],"Using":[116],"method,":[118],"4,000":[121],"10":[125],"types":[126,137],"cancer.":[128],"highly":[132],"effective":[133],"classifying":[135],"different":[136],"deriving":[142],"potential":[143,149],"prognostic":[144,150],"pairs.":[146],"particular,":[148],"pairs":[152],"derived":[153],"were":[157],"powerful":[158],"predicting":[160],"survival":[162],"time":[163],"patients.":[166,180],"This":[167],"approach":[168],"will":[169],"help":[170],"identify":[171],"predict":[176],"prognosis":[177]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}