{"id":"https://openalex.org/W2106900741","doi":"https://doi.org/10.1186/1471-2164-5-59","title":"Combined analysis of expression data and transcription factor binding sites in the yeast genome","display_name":"Combined analysis of expression data and transcription factor binding sites in the yeast genome","publication_year":2004,"publication_date":"2004-08-26","ids":{"openalex":"https://openalex.org/W2106900741","doi":"https://doi.org/10.1186/1471-2164-5-59","mag":"2106900741","pmid":"https://pubmed.ncbi.nlm.nih.gov/15331021","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/517709"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2164-5-59","doi":"https://doi.org/10.1186/1471-2164-5-59","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2164-5-59","pdf_url":"https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/1471-2164-5-59","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,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-140","russia-white-list-1","vabb-shw"],"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"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/1471-2164-5-59","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008849244","display_name":"Vijayalakshmi H. Nagaraj","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vijayalakshmi H Nagaraj","raw_affiliation_strings":["BioMaPS Institute, Rutgers University, Piscataway, NJ 08854, USA. viji@waksman.rutgers.edu","BioMaPS Institute, Rutgers University, Piscataway, NJ, 08854, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioMaPS Institute, Rutgers University, Piscataway, NJ 08854, USA. viji@waksman.rutgers.edu","institution_ids":["https://openalex.org/I102322142"]},{"raw_affiliation_string":"BioMaPS Institute, Rutgers University, Piscataway, NJ, 08854, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004796218","display_name":"Ruadhan A O'Flanagan","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ruadhan A O'Flanagan","raw_affiliation_strings":["Department of Physics and Astronomy, Rutgers University, Piscataway, NJ, 08854, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics and Astronomy, Rutgers University, Piscataway, NJ, 08854, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031158581","display_name":"Adrian R. N. E. Br\u00fcning","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adrian R Bruning","raw_affiliation_strings":["Waksman Institute and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, 08854, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Waksman Institute and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, 08854, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027452504","display_name":"Jonathan R. Mathias","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]},{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan R Mathias","raw_affiliation_strings":["Medical Sciences Center, University of Wisconsin, Madison, WI, 53706, USA","Waksman Institute and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, 08854, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Sciences Center, University of Wisconsin, Madison, WI, 53706, USA","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Waksman Institute and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, 08854, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013003121","display_name":"Andrew K. Vershon","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew K Vershon","raw_affiliation_strings":["Waksman Institute and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, 08854, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Waksman Institute and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, 08854, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066552315","display_name":"Anirvan M. Sengupta","orcid":"https://orcid.org/0000-0002-1080-0744","observed_orcids":["https://orcid.org/0000-0002-1080-0744"]},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Anirvan M Sengupta","raw_affiliation_strings":["BioMaPS Institute, Rutgers University, Piscataway, NJ, 08854, USA","Department of Physics and Astronomy, Rutgers University, Piscataway, NJ, 08854, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioMaPS Institute, Rutgers University, Piscataway, NJ, 08854, USA","institution_ids":["https://openalex.org/I102322142"]},{"raw_affiliation_string":"Department of Physics and Astronomy, Rutgers University, Piscataway, NJ, 08854, USA","institution_ids":["https://openalex.org/I102322142"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5066552315"],"corresponding_institution_ids":["https://openalex.org/I102322142"],"apc_list":{"value":3090,"currency":"USD","value_usd":3090},"apc_paid":{"value":3090,"currency":"USD","value_usd":3090},"fwci":0.8285,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.68643026,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":94},"biblio":{"volume":"5","issue":"1","first_page":"59","last_page":"59"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10497","display_name":"Fungal and yeast genetics research","score":0.638700008392334,"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/T10497","display_name":"Fungal and yeast genetics research","score":0.638700008392334,"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":0.30979999899864197,"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":0.016100000590085983,"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/transcription-factor-binding-sites","display_name":"transcription factor binding sites","score":0.9610000252723694},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"gene expression profiling","score":0.7839999794960022},{"id":"https://openalex.org/keywords/saccharomyces-cerevisiae","display_name":"Saccharomyces cerevisiae","score":0.8790000081062317},{"id":"https://openalex.org/keywords/transcriptional-repression","display_name":"transcriptional repression","score":0.8140000104904175},{"id":"https://openalex.org/keywords/promoter-regulation","display_name":"promoter regulation","score":0.5740000009536743},{"id":"https://openalex.org/keywords/co-regulation","display_name":"co-regulation","score":0.5849999785423279},{"id":"https://openalex.org/keywords/false-positive-reduction","display_name":"false positive reduction","score":0.5070000290870667}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8015130162239075},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6783303022384644},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.6681750416755676},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6633992195129395},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.6280895471572876},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5519850850105286},{"id":"https://openalex.org/C2777576037","wikidata":"https://www.wikidata.org/wiki/Q719725","display_name":"Saccharomyces cerevisiae","level":3,"score":0.5406633615493774},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.5096807479858398},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4906712770462036},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.46048223972320557},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.4601597785949707},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.45669183135032654},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.41252022981643677},{"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"D004171","descriptor_name":"Diploidy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D006238","descriptor_name":"Haploidy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011237","descriptor_name":"Predictive Value of Tests","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":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"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":true},{"descriptor_ui":"D015966","descriptor_name":"Gene Expression Regulation, Fungal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2164-5-59","doi":"https://doi.org/10.1186/1471-2164-5-59","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2164-5-59","pdf_url":"https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/1471-2164-5-59","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,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-140","russia-white-list-1","vabb-shw"],"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":"pmh:oai:pubmedcentral.nih.gov:517709","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/517709","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Genomics","raw_type":"Text"},{"id":"pmid:15331021","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15331021","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,"listed_in":[],"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":"Comparative Study"},{"id":"pmh:oai:doaj.org/article:e5be876a41104d6b96da23f69b182286","doi":null,"is_oa":false,"landing_page_url":"https://doaj.org/article/e5be876a41104d6b96da23f69b182286","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,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Genomics, Vol 5, Iss 1, p 59 (2004)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2164-5-59","doi":"https://doi.org/10.1186/1471-2164-5-59","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2164-5-59","pdf_url":"https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/1471-2164-5-59","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,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-140","russia-white-list-1","vabb-shw"],"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":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3717155376","display_name":"Combinatorial Control of Transcription in Yeast","funder_award_id":"R01GM049265","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2106900741.pdf","grobid_xml":"https://content.openalex.org/works/W2106900741.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W45292655","https://openalex.org/W1498410508","https://openalex.org/W1562374859","https://openalex.org/W1579786036","https://openalex.org/W1803509301","https://openalex.org/W1838513664","https://openalex.org/W1986748430","https://openalex.org/W2006220169","https://openalex.org/W2006873092","https://openalex.org/W2007710180","https://openalex.org/W2010108735","https://openalex.org/W2016812568","https://openalex.org/W2023450626","https://openalex.org/W2025562671","https://openalex.org/W2032548898","https://openalex.org/W2033825826","https://openalex.org/W2035564383","https://openalex.org/W2043839008","https://openalex.org/W2046278558","https://openalex.org/W2054624670","https://openalex.org/W2054640781","https://openalex.org/W2058682865","https://openalex.org/W2073727170","https://openalex.org/W2074204387","https://openalex.org/W2075900374","https://openalex.org/W2085640231","https://openalex.org/W2088243488","https://openalex.org/W2094917306","https://openalex.org/W2097390727","https://openalex.org/W2108420379","https://openalex.org/W2108818873","https://openalex.org/W2111497410","https://openalex.org/W2112247858","https://openalex.org/W2127593441","https://openalex.org/W2130494035","https://openalex.org/W2135000328","https://openalex.org/W2138871437","https://openalex.org/W2144710927","https://openalex.org/W2164935229","https://openalex.org/W2165011536","https://openalex.org/W2167190345","https://openalex.org/W2253910735","https://openalex.org/W2279351340","https://openalex.org/W4237493484","https://openalex.org/W4247420482","https://openalex.org/W4252564156"],"related_works":["https://openalex.org/W3083097828","https://openalex.org/W4226146228","https://openalex.org/W1753000577","https://openalex.org/W2167020833","https://openalex.org/W1579587866","https://openalex.org/W3142710889","https://openalex.org/W7095381799","https://openalex.org/W2034505818","https://openalex.org/W2108887668","https://openalex.org/W2029583014"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1],"analysis":[2,111],"of":[3,13,22,31,38,40,55,61,97,123,132,144,155,170,186,196,201,207,209,212],"gene":[4,43,57],"expression":[5,83],"using":[6],"DNA":[7],"microarrays":[8],"provides":[9],"genome":[10],"wide":[11],"profiles":[12],"the":[14,18,28,36,47,53,56,67,98,106,124,156,187,205],"genes":[15,104,118,146],"controlled":[16],"by":[17,46,93],"presence":[19],"or":[20,58,115],"absence":[21],"a":[23,33,41,77,130,142,176],"specific":[24,42,210],"transcription":[25,39,48,63,169],"factor.":[26],"However,":[27],"question":[29],"arises":[30],"whether":[32],"change":[34],"in":[35,105],"level":[37],"is":[44],"caused":[45],"factor":[49],"acting":[50],"directly":[51],"at":[52,66],"promoter":[54],"through":[59],"regulation":[60],"other":[62],"factors":[64],"working":[65],"promoter.":[68],"RESULTS:":[69],"To":[70],"address":[71],"this":[72,91],"problem":[73],"we":[74],"have":[75,89],"devised":[76],"computational":[78],"method":[79,174],"that":[80,119,165],"combines":[81],"microarray":[82],"and":[84],"site":[85],"preference":[86],"data.":[87],"We":[88,136],"tested":[90],"approach":[92],"identifying":[94],"functional":[95],"targets":[96,122,154],"a1-alpha2":[99,125,157,162],"complex,":[100,126,158],"which":[101,147],"represses":[102],"haploid-specific":[103,117,145],"yeast":[107],"Saccharomyces":[108],"cerevisiae.":[109],"Our":[110,173],"identified":[112],"many":[113],"known":[114],"suspected":[116],"are":[120],"direct":[121,153],"as":[127,129,159,161],"well":[128,160],"number":[131,143],"previously":[133],"uncharacterized":[134],"targets.":[135],"were":[137],"also":[138],"able":[139],"to":[140,151,184,203],"identify":[141],"do":[148,166],"not":[149,167],"appear":[150],"be":[152],"target":[163],"sites":[164],"repress":[168],"nearby":[171],"genes.":[172,213],"has":[175],"much":[177],"lower":[178],"false":[179],"positive":[180],"rate":[181],"when":[182],"compared":[183],"some":[185],"conventional":[188],"bioinformatic":[189],"approaches.":[190],"CONCLUSIONS:":[191],"These":[192],"findings":[193],"show":[194],"advantages":[195],"combining":[197],"these":[198],"two":[199],"forms":[200],"data":[202],"investigate":[204],"mechanism":[206],"co-regulation":[208],"sets":[211]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}