{"id":"https://openalex.org/W4392002097","doi":"https://doi.org/10.1186/s13040-024-00357-1","title":"A network-based drug prioritization and combination analysis for the MEK5/ERK5 pathway in breast cancer","display_name":"A network-based drug prioritization and combination analysis for the MEK5/ERK5 pathway in breast cancer","publication_year":2024,"publication_date":"2024-02-21","ids":{"openalex":"https://openalex.org/W4392002097","doi":"https://doi.org/10.1186/s13040-024-00357-1","pmid":"https://pubmed.ncbi.nlm.nih.gov/38378612"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-024-00357-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-024-00357-1","pdf_url":"https://link.springer.com/content/pdf/10.1186/s13040-024-00357-1.pdf","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://link.springer.com/content/pdf/10.1186/s13040-024-00357-1.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008459218","display_name":"Regan Odongo","orcid":"https://orcid.org/0000-0002-7200-7477"},"institutions":[{"id":"https://openalex.org/I109297418","display_name":"Gebze Technical University","ror":"https://ror.org/01sdnnq10","country_code":"TR","type":"education","lineage":["https://openalex.org/I109297418"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Regan Odongo","raw_affiliation_strings":["Department of Bioengineering, Faculty of Engineering, Gebze Technical University, Gebze, Kocaeli, 41400, Turkey. odongoregan@gmail.com"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Faculty of Engineering, Gebze Technical University, Gebze, Kocaeli, 41400, Turkey. odongoregan@gmail.com","institution_ids":["https://openalex.org/I109297418"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002298062","display_name":"Asuman Demiroglu\u2010Zergeroglu","orcid":"https://orcid.org/0000-0001-6272-7158"},"institutions":[{"id":"https://openalex.org/I109297418","display_name":"Gebze Technical University","ror":"https://ror.org/01sdnnq10","country_code":"TR","type":"education","lineage":["https://openalex.org/I109297418"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Asuman Demiroglu-Zergeroglu","raw_affiliation_strings":["Department of Molecular Biology & Genetics, Faculty of Science, Gebze Technical University, Gebze, Kocaeli, 41400, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology & Genetics, Faculty of Science, Gebze Technical University, Gebze, Kocaeli, 41400, Turkey","institution_ids":["https://openalex.org/I109297418"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080425354","display_name":"Tunahan \u00c7ak\u0131r","orcid":"https://orcid.org/0000-0001-8262-4420"},"institutions":[{"id":"https://openalex.org/I109297418","display_name":"Gebze Technical University","ror":"https://ror.org/01sdnnq10","country_code":"TR","type":"education","lineage":["https://openalex.org/I109297418"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Tunahan \u00c7ak\u0131r","raw_affiliation_strings":["Department of Bioengineering, Faculty of Engineering, Gebze Technical University, Gebze, Kocaeli, 41400, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Faculty of Engineering, Gebze Technical University, Gebze, Kocaeli, 41400, Turkey","institution_ids":["https://openalex.org/I109297418"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5008459218"],"corresponding_institution_ids":["https://openalex.org/I109297418"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.1042,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.75329293,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"17","issue":"1","first_page":"5","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11533","display_name":"Melanoma and MAPK Pathways","score":0.7815999984741211,"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/T11533","display_name":"Melanoma and MAPK Pathways","score":0.7815999984741211,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.06889999657869339,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.02410000003874302,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/breast-cancer","display_name":"Breast cancer","score":0.6359835863113403},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5408755540847778},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4838515818119049},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.4789629280567169},{"id":"https://openalex.org/keywords/cancer-drugs","display_name":"Cancer drugs","score":0.4617592990398407},{"id":"https://openalex.org/keywords/prioritization","display_name":"Prioritization","score":0.45167604088783264},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.44984692335128784},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4438014626502991},{"id":"https://openalex.org/keywords/interaction-network","display_name":"Interaction network","score":0.4280543327331543},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3782428503036499},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.37318670749664307},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.2978188395500183},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.2611362040042877},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23270854353904724},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13851982355117798}],"concepts":[{"id":"https://openalex.org/C530470458","wikidata":"https://www.wikidata.org/wiki/Q128581","display_name":"Breast cancer","level":3,"score":0.6359835863113403},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5408755540847778},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4838515818119049},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.4789629280567169},{"id":"https://openalex.org/C3020340455","wikidata":"https://www.wikidata.org/wiki/Q974135","display_name":"Cancer drugs","level":3,"score":0.4617592990398407},{"id":"https://openalex.org/C2777615720","wikidata":"https://www.wikidata.org/wiki/Q11888847","display_name":"Prioritization","level":2,"score":0.45167604088783264},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.44984692335128784},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4438014626502991},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.4280543327331543},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3782428503036499},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.37318670749664307},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2978188395500183},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.2611362040042877},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23270854353904724},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13851982355117798},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.0},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13040-024-00357-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-024-00357-1","pdf_url":"https://link.springer.com/content/pdf/10.1186/s13040-024-00357-1.pdf","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:38378612","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38378612","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":"BioData mining","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10880212","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10880212","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10880212/pdf/13040_2024_Article_357.pdf","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":"BioData Min","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:8a168d4792bc44b3af34efabb6b235e0","is_oa":true,"landing_page_url":"https://doaj.org/article/8a168d4792bc44b3af34efabb6b235e0","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Mining, Vol 17, Iss 1, Pp 1-19 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13040-024-00357-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-024-00357-1","pdf_url":"https://link.springer.com/content/pdf/10.1186/s13040-024-00357-1.pdf","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.7400000095367432}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4392002097.pdf","grobid_xml":"https://content.openalex.org/works/W4392002097.grobid-xml"},"referenced_works_count":65,"referenced_works":["https://openalex.org/W1245681932","https://openalex.org/W1960984881","https://openalex.org/W1985259498","https://openalex.org/W1986041799","https://openalex.org/W1986553481","https://openalex.org/W1987816069","https://openalex.org/W2013246214","https://openalex.org/W2024913322","https://openalex.org/W2033591223","https://openalex.org/W2062533676","https://openalex.org/W2072655513","https://openalex.org/W2075376976","https://openalex.org/W2077028619","https://openalex.org/W2084016080","https://openalex.org/W2086492959","https://openalex.org/W2098509290","https://openalex.org/W2098784161","https://openalex.org/W2100761975","https://openalex.org/W2104843251","https://openalex.org/W2105455398","https://openalex.org/W2111758831","https://openalex.org/W2136155231","https://openalex.org/W2141224543","https://openalex.org/W2146512944","https://openalex.org/W2163129204","https://openalex.org/W2202954603","https://openalex.org/W2263739890","https://openalex.org/W2342256727","https://openalex.org/W2345356016","https://openalex.org/W2475056796","https://openalex.org/W2519842263","https://openalex.org/W2537679995","https://openalex.org/W2582457346","https://openalex.org/W2612084686","https://openalex.org/W2767891136","https://openalex.org/W2795989238","https://openalex.org/W2886512250","https://openalex.org/W2922229918","https://openalex.org/W2923005485","https://openalex.org/W2982940349","https://openalex.org/W3011072970","https://openalex.org/W3020127841","https://openalex.org/W3035496509","https://openalex.org/W3093286766","https://openalex.org/W3106785508","https://openalex.org/W3158868742","https://openalex.org/W3161685224","https://openalex.org/W3163945650","https://openalex.org/W3173171686","https://openalex.org/W3193378962","https://openalex.org/W3206012263","https://openalex.org/W4200080541","https://openalex.org/W4212981693","https://openalex.org/W4214728644","https://openalex.org/W4225571935","https://openalex.org/W4226073269","https://openalex.org/W4226144949","https://openalex.org/W4229780490","https://openalex.org/W4249747122","https://openalex.org/W4296301762","https://openalex.org/W4304196136","https://openalex.org/W4323665734","https://openalex.org/W4387767168","https://openalex.org/W4389794367","https://openalex.org/W4390585893"],"related_works":["https://openalex.org/W2506292322","https://openalex.org/W4283209547","https://openalex.org/W4367627632","https://openalex.org/W2184980933","https://openalex.org/W653452717","https://openalex.org/W2554445088","https://openalex.org/W2621003306","https://openalex.org/W2335661150","https://openalex.org/W4239572564","https://openalex.org/W2127864418"],"abstract_inverted_index":{"BACKGROUND:":[0],"Prioritizing":[1],"candidate":[2],"drugs":[3,86,135,163],"based":[4],"on":[5,50,96],"genome-wide":[6],"expression":[7],"data":[8],"is":[9,204],"an":[10],"emerging":[11],"approach":[12,31],"in":[13,45,61,119,136,168,175,179,199],"systems":[14],"pharmacology":[15,107,141],"due":[16],"to":[17,36,109,219],"its":[18],"holistic":[19],"perspective":[20],"for":[21,78,117,144,173,189],"preclinical":[22],"drug":[23,43,59,115,190],"evaluation.":[24],"In":[25],"the":[26,97,155,176,195,208],"current":[27],"study,":[28],"a":[29,55,104,186,212],"network-based":[30],"was":[32],"proposed":[33],"and":[34,40,72,85,113,192,206],"applied":[35,103,218],"prioritize":[37,110],"plant":[38,83,111,127],"polyphenols":[39,84,112],"identify":[41],"potential":[42,58,114],"combinations":[44,116],"breast":[46,81,120,137,169,180,200],"cancer.":[47,121,181,201],"We":[48],"focused":[49],"MEK5/ERK5":[51,98,177,196],"signalling":[52,99],"pathway":[53,178,198],"genes,":[54],"recently":[56],"identified":[57],"target":[60,145,158],"cancer":[62,138,170],"with":[63,139,149,162,194,211],"roles":[64],"spanning":[65],"major":[66],"carcinogenesis":[67],"processes.":[68],"RESULTS:":[69],"By":[70],"constructing":[71],"identifying":[73],"perturbed":[74],"protein-protein":[75],"interaction":[76],"networks":[77],"luminal":[79],"A":[80],"cancer,":[82],"from":[87],"transcriptome":[88],"data,":[89],"we":[90,102],"first":[91],"demonstrated":[92],"their":[93],"systemic":[94],"effects":[95],"pathway.":[100],"Subsequently,":[101],"pathway-specific":[105],"network":[106,146,159],"pipeline":[108],"use":[118,174],"Our":[122],"analysis":[123],"prioritized":[124,172],"genistein":[125],"among":[126],"polyphenols.":[128],"Drug":[129],"combination":[130,148,193],"simulations":[131],"predicted":[132],"several":[133],"FDA-approved":[134],"well-established":[140],"as":[142],"candidates":[143],"synergistic":[147],"genistein.":[150],"This":[151,183],"study":[152,184],"also":[153],"highlights":[154],"concept":[156],"of":[157],"enhancer":[160],"drugs,":[161],"previously":[164],"not":[165],"well":[166],"characterised":[167],"being":[171],"CONCLUSION:":[182],"proposes":[185],"computational":[187],"framework":[188],"prioritization":[191],"signaling":[197],"The":[202],"method":[203,214],"flexible":[205],"provides":[207],"scientific":[209],"community":[210],"robust":[213],"that":[215],"can":[216],"be":[217],"other":[220],"complex":[221],"diseases.":[222]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
