{"id":"https://openalex.org/W2133449910","doi":"https://doi.org/10.1093/bioinformatics/bti172","title":"Synergy of human Pol II core promoter elements revealed by statistical sequence analysis","display_name":"Synergy of human Pol II core promoter elements revealed by statistical sequence analysis","publication_year":2004,"publication_date":"2004-11-30","ids":{"openalex":"https://openalex.org/W2133449910","doi":"https://doi.org/10.1093/bioinformatics/bti172","mag":"2133449910","pmid":"https://pubmed.ncbi.nlm.nih.gov/15572469"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti172","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti172","pdf_url":null,"source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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","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/A5035299451","display_name":"Naum I. Gershenzon","orcid":"https://orcid.org/0000-0001-7955-277X"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"N. I. Gershenzon","raw_affiliation_strings":["Department of Biomedical Informatics, The Ohio State University, 3184 Graves Hall, 333 W. 10th Avenue, Columbus, OH 43210, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, The Ohio State University, 3184 Graves Hall, 333 W. 10th Avenue, Columbus, OH 43210, USA","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026485637","display_name":"I. P. Ioshikhes","orcid":null},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"I. P. Ioshikhes","raw_affiliation_strings":["Department of Biomedical Informatics, The Ohio State University 3184 Graves Hall, 333 W. 10th Avenue, Columbus, OH 43210, USA","Department of Biomedical Informatics, The Ohio State University, 3184 Graves Hall, 333 W. 10th Avenue, Columbus, OH 43210, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, The Ohio State University 3184 Graves Hall, 333 W. 10th Avenue, Columbus, OH 43210, USA","institution_ids":["https://openalex.org/I52357470"]},{"raw_affiliation_string":"Department of Biomedical Informatics, The Ohio State University, 3184 Graves Hall, 333 W. 10th Avenue, Columbus, OH 43210, USA","institution_ids":["https://openalex.org/I52357470"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5035299451"],"corresponding_institution_ids":["https://openalex.org/I52357470"],"apc_list":null,"apc_paid":null,"fwci":3.0817,"has_fulltext":false,"cited_by_count":136,"citation_normalized_percentile":{"value":0.92030842,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":93,"max":99},"biblio":{"volume":"21","issue":"8","first_page":"1295","last_page":"1300"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9060999751091003,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9060999751091003,"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":0.02410000003874302,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.014299999922513962,"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/tata-box","display_name":"TATA box","score":0.866302490234375},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.85576331615448},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.6072606444358826},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.58719801902771},{"id":"https://openalex.org/keywords/transcription-factor-ii-a","display_name":"Transcription factor II A","score":0.5046905279159546},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4958284795284271},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4730091392993927},{"id":"https://openalex.org/keywords/response-element","display_name":"Response element","score":0.43390417098999023},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.4275960624217987},{"id":"https://openalex.org/keywords/general-transcription-factor","display_name":"General transcription factor","score":0.41103214025497437},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.33910825848579407},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2921900451183319},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1508370339870453}],"concepts":[{"id":"https://openalex.org/C65888428","wikidata":"https://www.wikidata.org/wiki/Q1413955","display_name":"TATA box","level":5,"score":0.866302490234375},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.85576331615448},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.6072606444358826},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.58719801902771},{"id":"https://openalex.org/C44498088","wikidata":"https://www.wikidata.org/wiki/Q14878255","display_name":"Transcription factor II A","level":5,"score":0.5046905279159546},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4958284795284271},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4730091392993927},{"id":"https://openalex.org/C132376346","wikidata":"https://www.wikidata.org/wiki/Q7315962","display_name":"Response element","level":5,"score":0.43390417098999023},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4275960624217987},{"id":"https://openalex.org/C144825837","wikidata":"https://www.wikidata.org/wiki/Q2316030","display_name":"General transcription factor","level":5,"score":0.41103214025497437},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.33910825848579407},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2921900451183319},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1508370339870453},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D004257","descriptor_name":"DNA Polymerase II","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004257","descriptor_name":"DNA Polymerase II","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004257","descriptor_name":"DNA Polymerase II","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020218","descriptor_name":"Response Elements","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020218","descriptor_name":"Response Elements","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020218","descriptor_name":"Response Elements","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bti172","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti172","pdf_url":null,"source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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:15572469","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15572469","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":"Evaluation Study"},{"id":"pmh:oai:corescholar.libraries.wright.edu:physics-1603","is_oa":false,"landing_page_url":"https://corescholar.libraries.wright.edu/physics/557","pdf_url":null,"source":{"id":"https://openalex.org/S2737205702","display_name":"Journal of Bioresource Management","issn_l":"2309-3854","issn":["2309-3854"],"is_oa":false,"is_in_doaj":true,"is_core":false,"host_organization":"https://openalex.org/P4310316536","host_organization_name":"Bioresource Research Center (BRC), Islamabad","host_organization_lineage":["https://openalex.org/P4310316536"],"host_organization_lineage_names":["Bioresource Research Center (BRC), Islamabad"],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Physics Faculty Publications","raw_type":"text"},{"id":"pmh:oai:works.bepress.com:naum_gershenzon-1027","is_oa":false,"landing_page_url":"https://works.bepress.com/naum_gershenzon/28","pdf_url":null,"source":{"id":"https://openalex.org/S2737205702","display_name":"Journal of Bioresource Management","issn_l":"2309-3854","issn":["2309-3854"],"is_oa":false,"is_in_doaj":true,"is_core":false,"host_organization":"https://openalex.org/P4310316536","host_organization_name":"Bioresource Research Center (BRC), Islamabad","host_organization_lineage":["https://openalex.org/P4310316536"],"host_organization_lineage_names":["Bioresource Research Center (BRC), Islamabad"],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Naum I. Gershenzon","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1529355444","https://openalex.org/W1577890972","https://openalex.org/W1816380050","https://openalex.org/W1974551833","https://openalex.org/W1988795249","https://openalex.org/W1990115520","https://openalex.org/W1999966058","https://openalex.org/W2006322387","https://openalex.org/W2006439752","https://openalex.org/W2011282682","https://openalex.org/W2027465760","https://openalex.org/W2047366906","https://openalex.org/W2052708514","https://openalex.org/W2054852737","https://openalex.org/W2061970520","https://openalex.org/W2071984843","https://openalex.org/W2081290562","https://openalex.org/W2084748297","https://openalex.org/W2085592229","https://openalex.org/W2095526875","https://openalex.org/W2096567462","https://openalex.org/W2097920884","https://openalex.org/W2098919421","https://openalex.org/W2101690350","https://openalex.org/W2124220434","https://openalex.org/W2127201083","https://openalex.org/W2128795978","https://openalex.org/W2154854793","https://openalex.org/W2162647736","https://openalex.org/W2164154631","https://openalex.org/W2166464288","https://openalex.org/W2170698318","https://openalex.org/W4232123327","https://openalex.org/W4237781946","https://openalex.org/W4246133277"],"related_works":["https://openalex.org/W1871847816","https://openalex.org/W2238886126","https://openalex.org/W2101341060","https://openalex.org/W2079124813","https://openalex.org/W2136592383","https://openalex.org/W2101898","https://openalex.org/W2065830290","https://openalex.org/W2005916961","https://openalex.org/W1971069125","https://openalex.org/W2034384738"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,115],"subject":[2],"of":[3,9,13,20,23,33,43,46,60,70,124,134,157,159],"our":[4],"paper":[5],"is":[6,117,146,177],"bioinformatics":[7],"analysis":[8],"the":[10,44,55,68,125,132,135,143,160,164],"distinguishing":[11],"features":[12],"human":[14],"promoter":[15,25,51,62,72],"DNA":[16],"sequences,":[17],"in":[18,128,163],"particular":[19,41],"synergetic":[21,100],"combinations":[22,69,127],"core":[24,61,71,161],"elements":[26,73,162],"therein.":[27],"We":[28,138],"suppose":[29],"that":[30,142],"specific":[31],"scenarios":[32],"transcription":[34,48,168],"initiation":[35],"are":[36],"essentially":[37],"related":[38],"to":[39,67],"various":[40],"implementations":[42],"interaction":[45],"basal":[47],"machinery":[49],"with":[50,112,131,166],"DNA,":[52],"depending":[53],"on":[54,119],"presence":[56],"and":[57,79,86,88,93,103,106,108,110,153],"mutual":[58],"positioning":[59],"elements.":[63],"RESULTS:":[64],"In":[65],"addition":[66],"previously":[74,151],"experimentally":[75],"confirmed":[76],"[TATA":[77],"box":[78],"Initiator":[80],"(Inr),":[81],"Downstream":[82],"Promoter":[83],"Element":[84],"(DPE)":[85],"Inr,":[87,104],"TFIIB":[89],"recognition":[90],"element":[91,145],"(BRE)":[92],"TATA":[94,109],"box]":[95],"we":[96],"propose":[97],"other":[98],"alternate":[99,126],"combinations:":[101],"BRE":[102,105,144],"DPE,":[107],"DPE":[111],"respective":[113],"models.":[114],"suggestion":[116],"based":[118],"a":[120],"high":[121],"statistical":[122],"significance":[123,133],"promoters,":[129],"comparable":[130],"known":[136],"combinations.":[137],"also":[139],"present":[140],"arguments":[141],"statistically":[147],"more":[148],"important":[149],"than":[150],"thought,":[152],"suggest":[154],"possible":[155],"mechanisms":[156],"action":[158],"promoters":[165],"multiple":[167],"start":[169],"sites.":[170],"CONTACT:":[171],"ioschikhes-1@medctr.osu.edu":[172],"SUPPLEMENTARY":[173],"INFORMATION:":[174],"Supplementary":[175],"information":[176],"available":[178],"at":[179],"http://bmi.osu.edu/~ilya/synergy/Gershenzon_SuppMat-R.pdf.":[180]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":11}],"updated_date":"2026-08-29T07:29:34.045763","created_date":"2025-10-10T00:00:00"}
