{"id":"https://openalex.org/W1998155250","doi":"https://doi.org/10.1093/nar/gkg517","title":"Dragon ERE Finder version 2: a tool for accurate detection and analysis of estrogen response elements in vertebrate genomes","display_name":"Dragon ERE Finder version 2: a tool for accurate detection and analysis of estrogen response elements in vertebrate genomes","publication_year":2003,"publication_date":"2003-06-24","ids":{"openalex":"https://openalex.org/W1998155250","doi":"https://doi.org/10.1093/nar/gkg517","mag":"1998155250","pmid":"https://pubmed.ncbi.nlm.nih.gov/12824376"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkg517","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg517","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3605/9487135/gkg517.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/nar/article-pdf/31/13/3605/9487135/gkg517.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055569646","display_name":"Vladimir B. Baji\u0107","orcid":"https://orcid.org/0000-0001-5435-4750"},"institutions":[{"id":"https://openalex.org/I3005327000","display_name":"Institute for Infocomm Research","ror":"https://ror.org/053rfa017","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I3005327000","https://openalex.org/I91275662"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"V. B. Bajic","raw_affiliation_strings":["Knowledge Extraction Laboratory, Institute for Infocomm Research, Singapore 119613. bajicv@i2r.a-star.edu.sg","Knowledge Extraction Laboratory, Institute for Infocomm Research, Singapore 119613"],"affiliations":[{"raw_affiliation_string":"Knowledge Extraction Laboratory, Institute for Infocomm Research, Singapore 119613. bajicv@i2r.a-star.edu.sg","institution_ids":["https://openalex.org/I3005327000"]},{"raw_affiliation_string":"Knowledge Extraction Laboratory, Institute for Infocomm Research, Singapore 119613","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5055569646"],"corresponding_institution_ids":["https://openalex.org/I3005327000"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":null,"fwci":4.2322,"has_fulltext":false,"cited_by_count":123,"citation_normalized_percentile":{"value":0.94978053,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"31","issue":"13","first_page":"3605","last_page":"3607"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9969000220298767,"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":0.9969000220298767,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.995199978351593,"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/T10756","display_name":"Estrogen and related hormone effects","score":0.989799976348877,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/biology","display_name":"Biology","score":0.8797022104263306},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6573376059532166},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.625343382358551},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.6117340326309204},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.6004047989845276},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5840316414833069},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.4474678337574005},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.43592357635498047},{"id":"https://openalex.org/keywords/human-genome","display_name":"Human genome","score":0.41560259461402893},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.11784791946411133}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8797022104263306},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6573376059532166},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.625343382358551},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.6117340326309204},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6004047989845276},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5840316414833069},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.4474678337574005},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.43592357635498047},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.41560259461402893},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11784791946411133}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004967","descriptor_name":"Estrogens","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D004967","descriptor_name":"Estrogens","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D004967","descriptor_name":"Estrogens","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","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":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"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":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020218","descriptor_name":"Response Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020218","descriptor_name":"Response Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gkg517","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg517","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3605/9487135/gkg517.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:12824376","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12824376","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:europepmc.org:158799","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC168924","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:168924","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:168924","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/168924","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkg517","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg517","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3605/9487135/gkg517.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4099999964237213,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1998155250.pdf","grobid_xml":"https://content.openalex.org/works/W1998155250.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W1509151417","https://openalex.org/W1540390595","https://openalex.org/W1556160432","https://openalex.org/W1981686096","https://openalex.org/W1995235768","https://openalex.org/W2010123171","https://openalex.org/W2026443131","https://openalex.org/W2032284355","https://openalex.org/W2044252104","https://openalex.org/W2046554880","https://openalex.org/W2049716343","https://openalex.org/W2086260205","https://openalex.org/W2090993551","https://openalex.org/W2096329971","https://openalex.org/W2112444654","https://openalex.org/W2119747788","https://openalex.org/W2149475194","https://openalex.org/W2158714788","https://openalex.org/W2164260861","https://openalex.org/W2166898290","https://openalex.org/W2216094174"],"related_works":["https://openalex.org/W1969895229","https://openalex.org/W2108497208","https://openalex.org/W2146517458","https://openalex.org/W2379997263","https://openalex.org/W2367493320","https://openalex.org/W2131580913","https://openalex.org/W2133132048","https://openalex.org/W2125854412","https://openalex.org/W3083097828","https://openalex.org/W2796029694"],"abstract_inverted_index":{"We":[0],"present":[1],"a":[2,37,73,106],"unique":[3],"program":[4],"for":[5,52,68,75,102,124],"identification":[6],"of":[7,39,96,109],"estrogen":[8],"response":[9],"elements":[10],"(EREs)":[11],"in":[12,31],"genomic":[13],"DNA":[14],"and":[15,27,79,126],"related":[16],"analyses.":[17],"The":[18],"detection":[19],"algorithm":[20],"was":[21],"tested":[22],"on":[23,58],"several":[24],"large":[25],"datasets":[26],"makes":[28],"one":[29],"prediction":[30],"13":[32],"300":[33],"nt":[34],"while":[35],"achieving":[36],"sensitivity":[38],"83%.":[40],"Users":[41],"can":[42,89],"further":[43],"investigate":[44],"selected":[45],"regions":[46,82,95],"around":[47],"the":[48,59,76,92,112],"identified":[49,77,113],"ERE":[50,114,117],"patterns":[51],"transcription":[53],"factor":[54],"binding":[55],"sites":[56],"based":[57],"TRANSFAC":[60],"database.":[61],"It":[62],"is":[63,121],"also":[64],"possible":[65],"to":[66,111],"search":[67,90],"candidate":[69],"human":[70,100],"genes":[71,101],"with":[72],"match":[74],"EREs":[78],"their":[80],"flanking":[81],"within":[83],"EPD":[84],"annotated":[85],"promoters.":[86],"Additionally,":[87],"users":[88,128],"among":[91],"extended":[93],"promoter":[94],"approximately":[97],"11":[98],"000":[99],"those":[103],"that":[104],"have":[105],"high":[107],"degree":[108],"similarity":[110],"patterns.":[115],"Dragon":[116],"Finder":[118],"version":[119],"2":[120],"freely":[122],"available":[123],"academic":[125],"non-profit":[127],"(http://sdmc.lit.org.sg/ERE-V2/index).":[129]},"counts_by_year":[{"year":2023,"cited_by_count":4},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":6}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
