{"id":"https://openalex.org/W2143314089","doi":"https://doi.org/10.1186/1471-2164-13-s1-s3","title":"GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group","display_name":"GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group","publication_year":2012,"publication_date":"2012-01-01","ids":{"openalex":"https://openalex.org/W2143314089","doi":"https://doi.org/10.1186/1471-2164-13-s1-s3","mag":"2143314089","pmid":"https://pubmed.ncbi.nlm.nih.gov/22369687"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2164-13-s1-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2164-13-s1-s3","pdf_url":"https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/1471-2164-13-S1-S3","source":{"id":"https://openalex.org/S28614077","display_name":"BMC Genomics","issn_l":"1471-2164","issn":["1471-2164"],"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":"BMC Genomics","raw_type":"journal-article"},"type":"conference-abstract","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/1471-2164-13-S1-S3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110003739","display_name":"Tzong-Yi Lee","orcid":null},"institutions":[{"id":"https://openalex.org/I99908691","display_name":"Yuan Ze University","ror":"https://ror.org/01fv1ds98","country_code":"TW","type":"education","lineage":["https://openalex.org/I99908691"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Tzong-Yi Lee","raw_affiliation_strings":["Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan. francis@saturn.yzu.edu.tw","Department of Computer Science & Engineering, Yuan Ze University, Taoyuan, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan. francis@saturn.yzu.edu.tw","institution_ids":["https://openalex.org/I99908691"]},{"raw_affiliation_string":"Department of Computer Science & Engineering, Yuan Ze University, Taoyuan, Taiwan","institution_ids":["https://openalex.org/I99908691"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030196668","display_name":"Wen\u2010Chi Chang","orcid":"https://orcid.org/0000-0002-0347-1516"},"institutions":[{"id":"https://openalex.org/I91807558","display_name":"National Cheng Kung University","ror":"https://ror.org/01b8kcc49","country_code":"TW","type":"education","lineage":["https://openalex.org/I91807558"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Wen-Chi Chang","raw_affiliation_strings":["Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan","Institute of Tropical Plant Sciences National Cheng Kung University Tainan Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan","institution_ids":["https://openalex.org/I91807558"]},{"raw_affiliation_string":"Institute of Tropical Plant Sciences National Cheng Kung University Tainan Taiwan","institution_ids":["https://openalex.org/I91807558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013309172","display_name":"Justin Bo\u2010Kai Hsu","orcid":null},"institutions":[{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Justin Hsu","raw_affiliation_strings":["Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, Taiwan","Institute of Bioinformatics and Systems Biology, National Chiao-Tung University, Hsin-Chu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, Taiwan","institution_ids":["https://openalex.org/I148366613"]},{"raw_affiliation_string":"Institute of Bioinformatics and Systems Biology, National Chiao-Tung University, Hsin-Chu, Taiwan","institution_ids":["https://openalex.org/I148366613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008637858","display_name":"Tzu\u2010Hao Chang","orcid":"https://orcid.org/0000-0001-7011-3754"},"institutions":[{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Tzu-Hao Chang","raw_affiliation_strings":["Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, Taiwan","Institute of Bioinformatics and Systems Biology, National Chiao-Tung University, Hsin-Chu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, Taiwan","institution_ids":["https://openalex.org/I148366613"]},{"raw_affiliation_string":"Institute of Bioinformatics and Systems Biology, National Chiao-Tung University, Hsin-Chu, Taiwan","institution_ids":["https://openalex.org/I148366613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108524881","display_name":"Dray-Ming Shien","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dray-Ming Shien","raw_affiliation_strings":["Department of Multimedia and Game Science, Asia-Pacific Institute of Creativity, Miao-Li, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Multimedia and Game Science, Asia-Pacific Institute of Creativity, Miao-Li, Taiwan","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5030196668","https://openalex.org/A5110003739"],"corresponding_institution_ids":["https://openalex.org/I91807558","https://openalex.org/I99908691"],"apc_list":{"value":2690,"currency":"USD","value_usd":2690},"apc_paid":{"value":2690,"currency":"USD","value_usd":2690},"fwci":null,"has_fulltext":true,"cited_by_count":80,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"13","issue":"Suppl 1","first_page":"S3","last_page":"S3"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.5067999958992004,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.5067999958992004,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.4580000042915344,"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":0.007600000128149986,"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/biology","display_name":"Biology","score":0.7455458641052246},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.7275708913803101},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6602975130081177},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.6300845146179199},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.6237578392028809},{"id":"https://openalex.org/keywords/regulatory-sequence","display_name":"Regulatory sequence","score":0.5800087451934814},{"id":"https://openalex.org/keywords/tata-box","display_name":"TATA box","score":0.5518676042556763},{"id":"https://openalex.org/keywords/caat-box","display_name":"CAAT box","score":0.5333974361419678},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5164642333984375},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5029310584068298},{"id":"https://openalex.org/keywords/cpg-site","display_name":"CpG site","score":0.44969093799591064},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.4255450963973999},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2778010070323944},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.16253003478050232}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7455458641052246},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.7275708913803101},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6602975130081177},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.6300845146179199},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6237578392028809},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.5800087451934814},{"id":"https://openalex.org/C65888428","wikidata":"https://www.wikidata.org/wiki/Q1413955","display_name":"TATA box","level":5,"score":0.5518676042556763},{"id":"https://openalex.org/C179716448","wikidata":"https://www.wikidata.org/wiki/Q2508056","display_name":"CAAT box","level":5,"score":0.5333974361419678},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5164642333984375},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5029310584068298},{"id":"https://openalex.org/C140173407","wikidata":"https://www.wikidata.org/wiki/Q1138358","display_name":"CpG site","level":5,"score":0.44969093799591064},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.4255450963973999},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2778010070323944},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.16253003478050232}],"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":"D001482","descriptor_name":"Base Composition","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"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":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","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":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":"Q000502","qualifier_name":"physiology","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},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2164-13-s1-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2164-13-s1-s3","pdf_url":"https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/1471-2164-13-S1-S3","source":{"id":"https://openalex.org/S28614077","display_name":"BMC Genomics","issn_l":"1471-2164","issn":["1471-2164"],"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":"BMC Genomics","raw_type":"journal-article"},{"id":"pmid:22369687","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22369687","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 genomics","raw_type":null},{"id":"pmh:oai:europepmc.org:2592771","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3587379","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:f0c132eaf6284062867d2b64e16e7ee8","is_oa":true,"landing_page_url":"https://doaj.org/article/f0c132eaf6284062867d2b64e16e7ee8","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Genomics, Vol 13, Iss Suppl 1, p S3 (2012)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2164-13-s1-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2164-13-s1-s3","pdf_url":"https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/1471-2164-13-S1-S3","source":{"id":"https://openalex.org/S28614077","display_name":"BMC Genomics","issn_l":"1471-2164","issn":["1471-2164"],"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":"BMC Genomics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.44999998807907104,"display_name":"Life below water","id":"https://metadata.un.org/sdg/14"}],"awards":[{"id":"https://openalex.org/G2390933741","display_name":null,"funder_award_id":"NSC 99-2628-B-006-016-MY3","funder_id":"https://openalex.org/F4320321040","funder_display_name":"National Science Council"},{"id":"https://openalex.org/G3006427632","display_name":null,"funder_award_id":"NSC99","funder_id":"https://openalex.org/F4320321040","funder_display_name":"National Science Council"}],"funders":[{"id":"https://openalex.org/F4320321040","display_name":"National Science Council","ror":"https://ror.org/02kv4zf79"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2143314089.pdf","grobid_xml":"https://content.openalex.org/works/W2143314089.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W1220850065","https://openalex.org/W1520890006","https://openalex.org/W1825157170","https://openalex.org/W1965696530","https://openalex.org/W1972875048","https://openalex.org/W1973260612","https://openalex.org/W1974234299","https://openalex.org/W1977927254","https://openalex.org/W1979184235","https://openalex.org/W1981262837","https://openalex.org/W1987694360","https://openalex.org/W2001405084","https://openalex.org/W2003463914","https://openalex.org/W2004446162","https://openalex.org/W2013050589","https://openalex.org/W2013213258","https://openalex.org/W2027349221","https://openalex.org/W2034950225","https://openalex.org/W2051249540","https://openalex.org/W2055043387","https://openalex.org/W2057692691","https://openalex.org/W2075168304","https://openalex.org/W2075793022","https://openalex.org/W2082463698","https://openalex.org/W2084620487","https://openalex.org/W2094036688","https://openalex.org/W2096451658","https://openalex.org/W2097353028","https://openalex.org/W2098222328","https://openalex.org/W2105315497","https://openalex.org/W2112814753","https://openalex.org/W2113466606","https://openalex.org/W2115992869","https://openalex.org/W2123460634","https://openalex.org/W2124195715","https://openalex.org/W2130919037","https://openalex.org/W2134977238","https://openalex.org/W2135995702","https://openalex.org/W2137458297","https://openalex.org/W2142890842","https://openalex.org/W2153392439","https://openalex.org/W2153635508","https://openalex.org/W2157467374","https://openalex.org/W2158314946","https://openalex.org/W2161483827","https://openalex.org/W2162517990","https://openalex.org/W2164129281","https://openalex.org/W2164296513","https://openalex.org/W2165380507"],"related_works":["https://openalex.org/W2376546783","https://openalex.org/W2139995230","https://openalex.org/W2165053108","https://openalex.org/W2950174003","https://openalex.org/W2114041485","https://openalex.org/W2392370788","https://openalex.org/W2356348012","https://openalex.org/W2355712812","https://openalex.org/W4250682987","https://openalex.org/W2071137639"],"abstract_inverted_index":{"BACKGROUND:":[0],"Sequence":[1],"features":[2,43,92,116,223,238],"in":[3,8,93,102,117,127,259],"promoter":[4,95,119,218,235,245],"regions":[5],"are":[6,139,181,239],"involved":[7],"regulating":[9],"gene":[10,72,83,195,244],"transcription":[11,27],"initiation.":[12],"Although":[13],"numerous":[14,257],"computational":[15],"methods":[16],"have":[17],"been":[18],"developed":[19],"for":[20,36,213],"predicting":[21],"transcriptional":[22,84],"start":[23],"sites":[24,31],"(TSSs)":[25],"or":[26],"factor":[28],"(TF)":[29],"binding":[30],"(TFBSs),":[32],"they":[33],"lack":[34],"annotations":[35],"do":[37],"not":[38],"consider":[39],"some":[40],"important":[41],"regulatory":[42,91,115,222,237],"such":[44,145],"as":[45,146],"CpG":[46,147],"islands,":[47,148],"tandem":[48],"repeats,":[49],"the":[50,65,71,159,176,198],"TATA":[51],"box,":[52,54,56],"CCAAT":[53],"GC":[55,62],"over-represented":[57,151],"oligonucleotides,":[58],"DNA":[59,155],"stability,":[60,156],"and":[61,97,114,121,154,179,220,262],"content.":[63],"Additionally,":[64,205],"combinatorial":[66],"interaction":[67],"of":[68,100,105,124,194,200,215],"TFs":[69,101],"regulates":[70],"group":[73,104,193],"that":[74,89],"is":[75,107,268],"associated":[76],"with":[77,141],"same":[78],"expression":[79],"pattern.":[80],"To":[81],"investigate":[82],"regulation,":[85],"an":[86,206],"integrated":[87],"system":[88,187,267],"annotates":[90],"a":[94,103,118,131,166,192,252],"sequence":[96,208],"detects":[98],"co-regulation":[99],"genes":[106,129],"needed.":[108],"RESULTS:":[109],"This":[110],"work":[111],"identifies":[112],"TSSs":[113],"sequence,":[120],"recognizes":[122],"co-occurrence":[123,199],"cis-regulatory":[125],"elements":[126],"co-expressed":[128],"using":[130,165],"novel":[132,160],"system.":[133],"Three":[134],"well-known":[135],"TSS":[136],"prediction":[137],"tools":[138],"incorporated":[140],"orthologous":[142],"conserved":[143,221],"features,":[144],"nucleotide":[149],"composition,":[150],"hexamer":[152],"nucleotides,":[153],"to":[157,172,190,202,242],"construct":[158],"Gene":[161],"Promoter":[162],"Miner":[163],"(GPMiner)":[164],"support":[167],"vector":[168],"machine":[169],"(SVM).":[170],"According":[171],"five-fold":[173],"cross-validation":[174],"results,":[175],"predictive":[177],"sensitivity":[178],"specificity":[180],"both":[182],"roughly":[183],"80%.":[184],"The":[185,248,265],"proposed":[186,266],"allows":[188],"users":[189],"input":[191,207],"names/symbols,":[196],"enabling":[197],"TFBSs":[201],"be":[203,211,228],"determined.":[204],"can":[209,227],"also":[210],"analyzed":[212],"homogeneity":[214],"experimental":[216],"mammalian":[217],"sequences,":[219],"between":[224],"homologous":[225],"promoters":[226],"observed":[229],"through":[230],"cross-species":[231],"analysis.":[232],"After":[233],"identifying":[234],"regions,":[236],"visualized":[240],"graphically":[241],"facilitate":[243],"observations.":[246],"CONCLUSIONS:":[247],"GPMiner,":[249],"which":[250],"has":[251,256],"user-friendly":[253],"input/output":[254],"interface,":[255],"benefits":[258],"analyzing":[260],"human":[261],"mouse":[263],"promoters.":[264],"freely":[269],"available":[270],"at":[271],"http://GPMiner.mbc.nctu.edu.tw/.":[272]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":17},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}