{"id":"https://openalex.org/W2153920876","doi":"https://doi.org/10.1093/bioinformatics/bth927","title":"Predicting gene regulation by sigma factors in <i>Bacillus subtilis</i> from genome-wide data","display_name":"Predicting gene regulation by sigma factors in <i>Bacillus subtilis</i> from genome-wide data","publication_year":2004,"publication_date":"2004-07-19","ids":{"openalex":"https://openalex.org/W2153920876","doi":"https://doi.org/10.1093/bioinformatics/bth927","mag":"2153920876","pmid":"https://pubmed.ncbi.nlm.nih.gov/15262787"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth927","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth927","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5037842288","display_name":"Michiel de Hoon","orcid":"https://orcid.org/0000-0003-0489-2352"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]},{"id":"https://openalex.org/I161296585","display_name":"Tokyo University of Science","ror":"https://ror.org/05sj3n476","country_code":"JP","type":"education","lineage":["https://openalex.org/I161296585"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"M. J. L. de Hoon","raw_affiliation_strings":["Human Genome Center, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo, Japan. mdehoon@ims.u-tokyo.ac.jp"],"affiliations":[{"raw_affiliation_string":"Human Genome Center, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo, Japan. mdehoon@ims.u-tokyo.ac.jp","institution_ids":["https://openalex.org/I74801974","https://openalex.org/I161296585"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066711822","display_name":"Yuko Makita","orcid":"https://orcid.org/0000-0001-5745-6007"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Y. Makita","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090788230","display_name":"Seiya Imoto","orcid":"https://orcid.org/0000-0002-2989-308X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"S. Imoto","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100763634","display_name":"Kazuo Kobayashi","orcid":"https://orcid.org/0000-0002-7052-6759"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"K. Kobayashi","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007078528","display_name":"Naotaka Ogasawara","orcid":"https://orcid.org/0000-0002-7762-8512"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"N. Ogasawara","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054681585","display_name":"Kenta Nakai","orcid":"https://orcid.org/0000-0002-8721-8883"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"K. Nakai","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5088167618","display_name":"Satoru Miyano","orcid":"https://orcid.org/0000-0002-1753-6616"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"S. Miyano","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5037842288"],"corresponding_institution_ids":["https://openalex.org/I161296585","https://openalex.org/I74801974"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8186,"has_fulltext":false,"cited_by_count":26,"citation_normalized_percentile":{"value":0.70327358,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"20","issue":"suppl_1","first_page":"i101","last_page":"i108"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9997000098228455,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9997000098228455,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9994999766349792,"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"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9973999857902527,"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/logistic-regression","display_name":"Logistic regression","score":0.6566131114959717},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5815446972846985},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5195624828338623},{"id":"https://openalex.org/keywords/regression","display_name":"Regression","score":0.5186026096343994},{"id":"https://openalex.org/keywords/sigma","display_name":"Sigma","score":0.4833928644657135},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.46188515424728394},{"id":"https://openalex.org/keywords/sigma-factor","display_name":"Sigma factor","score":0.4518910050392151},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.43910717964172363},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4337882101535797},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.43155238032341003},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.42669808864593506},{"id":"https://openalex.org/keywords/bacillus-subtilis","display_name":"Bacillus subtilis","score":0.413044273853302},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36251795291900635},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.34675902128219604},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.34204810857772827},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.31901946663856506},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2270309031009674},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.21931463479995728},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.18959739804267883}],"concepts":[{"id":"https://openalex.org/C151956035","wikidata":"https://www.wikidata.org/wiki/Q1132755","display_name":"Logistic regression","level":2,"score":0.6566131114959717},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5815446972846985},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5195624828338623},{"id":"https://openalex.org/C83546350","wikidata":"https://www.wikidata.org/wiki/Q1139051","display_name":"Regression","level":2,"score":0.5186026096343994},{"id":"https://openalex.org/C2778049214","wikidata":"https://www.wikidata.org/wiki/Q7512234","display_name":"Sigma","level":2,"score":0.4833928644657135},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.46188515424728394},{"id":"https://openalex.org/C47319516","wikidata":"https://www.wikidata.org/wiki/Q306436","display_name":"Sigma factor","level":5,"score":0.4518910050392151},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.43910717964172363},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4337882101535797},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.43155238032341003},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.42669808864593506},{"id":"https://openalex.org/C2777272437","wikidata":"https://www.wikidata.org/wiki/Q131238","display_name":"Bacillus subtilis","level":3,"score":0.413044273853302},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36251795291900635},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34675902128219604},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.34204810857772827},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.31901946663856506},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2270309031009674},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.21931463479995728},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.18959739804267883},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"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":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012808","descriptor_name":"Sigma Factor","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012808","descriptor_name":"Sigma Factor","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012808","descriptor_name":"Sigma Factor","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bth927","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth927","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15262787","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15262787","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":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1481919380","https://openalex.org/W1554944419","https://openalex.org/W1559547793","https://openalex.org/W2004608252","https://openalex.org/W2009570821","https://openalex.org/W2018527742","https://openalex.org/W2039700732","https://openalex.org/W2067957566","https://openalex.org/W2073850887","https://openalex.org/W2079829409","https://openalex.org/W2082982706","https://openalex.org/W2090554117","https://openalex.org/W2108420379","https://openalex.org/W2108929880","https://openalex.org/W2116290764","https://openalex.org/W2120034091","https://openalex.org/W2149579404","https://openalex.org/W2611370172"],"related_works":["https://openalex.org/W4293061103","https://openalex.org/W3041516390","https://openalex.org/W1548672655","https://openalex.org/W2119248810","https://openalex.org/W2329565894","https://openalex.org/W2112264016","https://openalex.org/W4366691203","https://openalex.org/W2110929595","https://openalex.org/W1827772617","https://openalex.org/W2021511385"],"abstract_inverted_index":{"The":[0],"coregulation-based":[1],"supervised":[2],"learning":[3],"method":[4],"gave":[5],"the":[6,19,52],"most":[7],"accurate":[8],"prediction":[9],"of":[10,64],"sigma":[11],"factors":[12],"from":[13],"expression":[14,25],"data.":[15],"We":[16,50],"found":[17,40],"that":[18],"logistic":[20,36],"regression":[21,37],"model":[22],"effectively":[23],"combines":[24],"data":[26],"with":[27],"sequence":[28],"information.":[29],"In":[30],"a":[31,60],"genome-wide":[32],"search,":[33],"highly":[34],"significant":[35],"scores":[38],"were":[39],"for":[41],"several":[42],"genes":[43],"whose":[44],"transcriptional":[45],"regulation":[46],"is":[47],"currently":[48],"unknown.":[49],"provide":[51],"corresponding":[53],"RNA":[54],"polymerase":[55],"binding":[56],"sites":[57],"to":[58],"enable":[59],"straightforward":[61],"experimental":[62],"verification":[63],"these":[65],"predictions.":[66]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2016-06-24T00:00:00"}
