{"id":"https://openalex.org/W2561772691","doi":"https://doi.org/10.1186/s12918-016-0357-1","title":"Gene-microRNA network module analysis for ovarian cancer","display_name":"Gene-microRNA network module analysis for ovarian cancer","publication_year":2016,"publication_date":"2016-12-01","ids":{"openalex":"https://openalex.org/W2561772691","doi":"https://doi.org/10.1186/s12918-016-0357-1","mag":"2561772691","pmid":"https://pubmed.ncbi.nlm.nih.gov/28155675"},"language":"en","primary_location":{"id":"doi:10.1186/s12918-016-0357-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-016-0357-1","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-016-0357-1","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-016-0357-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024866341","display_name":"Shuqin Zhang","orcid":"https://orcid.org/0000-0001-8223-844X"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shuqin Zhang","raw_affiliation_strings":["Center for Computational Systems Biology, School of Mathematical Sciences, Fudan University, No.220 Handan Road, Shanghai, 200433, China. zhangs@fudan.edu.cn","Center for Computational Systems Biology, School of Mathematical Sciences, Fudan University, No.220 Handan Road, Shanghai, 200433, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Systems Biology, School of Mathematical Sciences, Fudan University, No.220 Handan Road, Shanghai, 200433, China. zhangs@fudan.edu.cn","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Center for Computational Systems Biology, School of Mathematical Sciences, Fudan University, No.220 Handan Road, Shanghai, 200433, China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010561682","display_name":"Michael K. Ng","orcid":"https://orcid.org/0000-0001-6833-5227"},"institutions":[{"id":"https://openalex.org/I80804394","display_name":"Southwest Baptist University","ror":"https://ror.org/02dgbcj80","country_code":"US","type":"education","lineage":["https://openalex.org/I80804394"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael K. Ng","raw_affiliation_strings":["Department of Mathematics, Hongkong Baptist University, Kowloon Tong, Hongkong, Hongkong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Hongkong Baptist University, Kowloon Tong, Hongkong, Hongkong","institution_ids":["https://openalex.org/I80804394"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5024866341"],"corresponding_institution_ids":["https://openalex.org/I24943067"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":0.9437,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.73485795,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"10","issue":"S4","first_page":"117","last_page":"117"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":0.6991999745368958,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10062","display_name":"MicroRNA in disease regulation","score":0.6991999745368958,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.1362999975681305,"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":0.052400000393390656,"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/microrna","display_name":"microRNA","score":0.8511337041854858},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.7023900747299194},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6817240715026855},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6709138751029968},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6428481340408325},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5220280289649963},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.5215237736701965},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5162227153778076},{"id":"https://openalex.org/keywords/kegg","display_name":"KEGG","score":0.5038802027702332},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.42354604601860046},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.34156447649002075},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.30831286311149597},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.11881116032600403}],"concepts":[{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.8511337041854858},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.7023900747299194},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6817240715026855},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6709138751029968},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6428481340408325},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5220280289649963},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.5215237736701965},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5162227153778076},{"id":"https://openalex.org/C152724338","wikidata":"https://www.wikidata.org/wiki/Q909442","display_name":"KEGG","level":5,"score":0.5038802027702332},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.42354604601860046},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.34156447649002075},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30831286311149597},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.11881116032600403}],"mesh":[{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","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":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","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}],"locations_count":3,"locations":[{"id":"doi:10.1186/s12918-016-0357-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-016-0357-1","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-016-0357-1","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:28155675","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28155675","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":"BMC systems biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5259869","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5259869","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12918-016-0357-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-016-0357-1","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-016-0357-1","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.6499999761581421}],"awards":[{"id":"https://openalex.org/G2498570045","display_name":null,"funder_award_id":"13ZR1403600","funder_id":"https://openalex.org/F4320309612","funder_display_name":"Natural Science Foundation of Shanghai"},{"id":"https://openalex.org/G3180573523","display_name":null,"funder_award_id":"11471082","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320309612","display_name":"Natural Science Foundation of Shanghai","ror":null},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2561772691.pdf","grobid_xml":"https://content.openalex.org/works/W2561772691.grobid-xml"},"referenced_works_count":52,"referenced_works":["https://openalex.org/W1967515816","https://openalex.org/W1974352012","https://openalex.org/W1975021063","https://openalex.org/W2000491596","https://openalex.org/W2001508508","https://openalex.org/W2002995168","https://openalex.org/W2006079840","https://openalex.org/W2011458493","https://openalex.org/W2011566302","https://openalex.org/W2012041376","https://openalex.org/W2017426710","https://openalex.org/W2017620474","https://openalex.org/W2028962637","https://openalex.org/W2032766715","https://openalex.org/W2034595398","https://openalex.org/W2042865509","https://openalex.org/W2044068890","https://openalex.org/W2053003053","https://openalex.org/W2057100799","https://openalex.org/W2060705109","https://openalex.org/W2074821116","https://openalex.org/W2077475358","https://openalex.org/W2080551186","https://openalex.org/W2095619968","https://openalex.org/W2103570076","https://openalex.org/W2104806799","https://openalex.org/W2107180520","https://openalex.org/W2109761160","https://openalex.org/W2110101814","https://openalex.org/W2111209092","https://openalex.org/W2113390076","https://openalex.org/W2121412124","https://openalex.org/W2123106337","https://openalex.org/W2130388134","https://openalex.org/W2130410032","https://openalex.org/W2133465414","https://openalex.org/W2134245005","https://openalex.org/W2134497014","https://openalex.org/W2137248444","https://openalex.org/W2138664009","https://openalex.org/W2141350766","https://openalex.org/W2142434250","https://openalex.org/W2143693563","https://openalex.org/W2146771296","https://openalex.org/W2155874171","https://openalex.org/W2158217645","https://openalex.org/W2161774774","https://openalex.org/W2170951627","https://openalex.org/W2171260596","https://openalex.org/W2171698535","https://openalex.org/W2310034942","https://openalex.org/W2597632520"],"related_works":["https://openalex.org/W2158714033","https://openalex.org/W78967844","https://openalex.org/W3213185671","https://openalex.org/W4210989272","https://openalex.org/W4386628104","https://openalex.org/W4206945140","https://openalex.org/W2130939068","https://openalex.org/W3163717165","https://openalex.org/W2509687359","https://openalex.org/W2114466827"],"abstract_inverted_index":{"BACKGROUND:":[0],"MicroRNAs":[1],"(miRNAs)":[2],"are":[3,178,216,254],"involved":[4],"in":[5,119,131,212],"many":[6,27],"biological":[7],"processes":[8],"by":[9,181],"regulating":[10],"post-transcriptional":[11],"gene":[12,56,78,168],"expression.":[13],"The":[14,47,175,243],"alterations":[15],"of":[16,49,77,116,201,233,259],"the":[17,34,38,66,74,85,93,117,120,129,132,139,152,158,198,208,230,241],"regulatory":[18,36],"pathways":[19],"can":[20,247],"cause":[21],"different":[22,257],"diseases":[23],"including":[24],"cancer.":[25,222],"Although":[26],"works":[28],"have":[29],"been":[30],"done":[31],"to":[32,53,64,91,100,126,150,160,250,256],"study":[33,51,101,225],"gene-miRNA":[35,82,87,142],"network,":[37],"intertwined":[39],"relationship":[40],"is":[41,52],"far":[42],"from":[43],"being":[44],"fully":[45],"understood.":[46],"objective":[48],"this":[50,107],"integrate":[54],"both":[55,128,167],"expression":[57,169,173],"data":[58,61,170],"and":[59,84,104,134,138,171,185,196,210,235],"miRNA":[60,80,172,182],"so":[62,98],"as":[63,99],"explore":[65],"complex":[67],"relationships":[68],"among":[69],"them.":[70],"METHODS:":[71],"By":[72],"integrating":[73],"networks":[75,137],"consisting":[76,232],"coexpression,":[79,81,83],"known":[86],"interactions,":[88],"we":[89,109],"aim":[90],"find":[92,127],"most":[94],"connected":[95,141],"network":[96],"modules":[97,118,130,177,215],"their":[102],"functions":[103],"properties.":[105],"In":[106],"paper,":[108],"proposed":[110,244],"an":[111],"optimization":[112,153],"model":[113,124],"for":[114],"identification":[115],"integrated":[121],"networks.":[122,260],"This":[123,224],"tries":[125],"gene-gene":[133],"miRNA-miRNA":[135],"coexpression":[136],"densely":[140],"subneworks.":[143],"An":[144],"approximation":[145],"computational":[146,245],"method":[147,159,191,246],"was":[148],"developed":[149],"solve":[151],"problem.":[154],"RESULTS:":[155],"We":[156,188,204],"applied":[157,249],"556":[161],"human":[162],"ovarian":[163,221],"cancer":[164],"samples":[165],"with":[166,192,218,237],"data.":[174],"identified":[176,214],"significantly":[179],"enriched":[180],"clusters,":[183],"GO-BPs,":[184],"KEGG":[186],"pathways.":[187],"compared":[189],"our":[190,202,213],"some":[193],"existing":[194],"methods":[195],"showed":[197,206],"better":[199],"performance":[200],"method.":[203],"also":[205],"that":[207,229,253],"miRNAs":[209,236],"genes":[211,234],"associated":[217],"cancers,":[219],"especially":[220],"CONCLUSIONS:":[223],"provides":[226],"strong":[227],"support":[228],"subnetworks":[231],"close":[238],"interactions":[239],"contribute":[240],"cancers.":[242],"be":[248],"other":[251],"studies":[252],"related":[255],"types":[258]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":5}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}