{"id":"https://openalex.org/W2127860120","doi":"https://doi.org/10.1186/1471-2105-9-484","title":"Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation","display_name":"Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation","publication_year":2008,"publication_date":"2008-11-17","ids":{"openalex":"https://openalex.org/W2127860120","doi":"https://doi.org/10.1186/1471-2105-9-484","mag":"2127860120","pmid":"https://pubmed.ncbi.nlm.nih.gov/19014636"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-9-484","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-484","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-484","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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 Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-484","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083732869","display_name":"Jakub Orzechowski Westholm","orcid":"https://orcid.org/0000-0002-6849-6220"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]},{"id":"https://openalex.org/I223464139","display_name":"Linnaeus University","ror":"https://ror.org/00j9qag85","country_code":"SE","type":"education","lineage":["https://openalex.org/I223464139"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Jakub Orzechowski Westholm","raw_affiliation_strings":["The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden. jakub@lcb.uu.se","The Linnaeus Centre for Bioinformatics, Uppsala University BMC, Uppsala, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden. jakub@lcb.uu.se","institution_ids":["https://openalex.org/I123387679"]},{"raw_affiliation_string":"The Linnaeus Centre for Bioinformatics, Uppsala University BMC, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679","https://openalex.org/I223464139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064720631","display_name":"Feifei Xu","orcid":"https://orcid.org/0000-0003-1946-1520"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]},{"id":"https://openalex.org/I223464139","display_name":"Linnaeus University","ror":"https://ror.org/00j9qag85","country_code":"SE","type":"education","lineage":["https://openalex.org/I223464139"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Feifei Xu","raw_affiliation_strings":["The Linnaeus Centre for Bioinformatics, Uppsala University, BMC, Box 598, SE-751 24, Uppsala, Sweden","The Linnaeus Centre for Bioinformatics, Uppsala University BMC, Uppsala, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Linnaeus Centre for Bioinformatics, Uppsala University, BMC, Box 598, SE-751 24, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679"]},{"raw_affiliation_string":"The Linnaeus Centre for Bioinformatics, Uppsala University BMC, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679","https://openalex.org/I223464139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049417333","display_name":"Hans Ronne","orcid":"https://orcid.org/0000-0002-1645-6091"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Hans Ronne","raw_affiliation_strings":["Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, SE-751 23, Uppsala, Sweden","Dept of Medical Biochemistry and Microbiology, Uppsala University, BMC, Uppsala, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, SE-751 23, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679"]},{"raw_affiliation_string":"Dept of Medical Biochemistry and Microbiology, Uppsala University, BMC, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050406527","display_name":"Jan Komorowski","orcid":"https://orcid.org/0000-0002-0766-8789"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]},{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL","SE"],"is_corresponding":true,"raw_author_name":"Jan Komorowski","raw_affiliation_strings":["Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, 02-106, Warsaw, Poland","The Linnaeus Centre for Bioinformatics, Uppsala University, BMC, Box 598, SE-751 24, Uppsala, Sweden","Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Warsaw, Poland","The Linnaeus Centre for Bioinformatics, Uppsala University,BMC, Uppsala, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, 02-106, Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"The Linnaeus Centre for Bioinformatics, Uppsala University, BMC, Box 598, SE-751 24, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679"]},{"raw_affiliation_string":"Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"The Linnaeus Centre for Bioinformatics, Uppsala University,BMC, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5050406527"],"corresponding_institution_ids":["https://openalex.org/I123387679","https://openalex.org/I4654613"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.1701,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.77590821,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"9","issue":"1","first_page":"484","last_page":"484"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9488000273704529,"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":0.9488000273704529,"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/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.031700000166893005,"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":0.0035000001080334187,"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":0.6002224683761597},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5910309553146362},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5858433842658997},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.5656481385231018},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.5605754256248474},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.5200843214988708},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5151728391647339},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.5029260516166687},{"id":"https://openalex.org/keywords/nucleosome","display_name":"Nucleosome","score":0.45012545585632324},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.43721941113471985},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.4202972650527954},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.41393494606018066},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4100390672683716},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.34278637170791626},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.3162253499031067}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6002224683761597},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5910309553146362},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5858433842658997},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.5656481385231018},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.5605754256248474},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.5200843214988708},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5151728391647339},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.5029260516166687},{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.45012545585632324},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.43721941113471985},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.4202972650527954},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.41393494606018066},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4100390672683716},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34278637170791626},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.3162253499031067},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","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},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","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":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015966","descriptor_name":"Gene Expression Regulation, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015966","descriptor_name":"Gene Expression Regulation, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015966","descriptor_name":"Gene Expression Regulation, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","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":4,"locations":[{"id":"doi:10.1186/1471-2105-9-484","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-484","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-484","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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 Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19014636","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19014636","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 bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2629780","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2629780","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,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:03088006314b44a1bb609c7a844ba735","is_oa":true,"landing_page_url":"https://doaj.org/article/03088006314b44a1bb609c7a844ba735","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 Bioinformatics, Vol 9, Iss 1, p 484 (2008)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-9-484","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-484","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-484","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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 Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320940","display_name":"Stiftelsen f\u00f6r\u00a0Strategisk Forskning","ror":"https://ror.org/044wr7g58"},{"id":"https://openalex.org/F4320322327","display_name":"Knut och Alice Wallenbergs Stiftelse","ror":"https://ror.org/004hzzk67"},{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2127860120.pdf","grobid_xml":"https://content.openalex.org/works/W2127860120.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W1528905581","https://openalex.org/W1719858377","https://openalex.org/W1867995571","https://openalex.org/W1996270170","https://openalex.org/W2000424161","https://openalex.org/W2007969038","https://openalex.org/W2032739790","https://openalex.org/W2045159582","https://openalex.org/W2073727170","https://openalex.org/W2073850887","https://openalex.org/W2080498142","https://openalex.org/W2084620487","https://openalex.org/W2096280725","https://openalex.org/W2097396311","https://openalex.org/W2098222328","https://openalex.org/W2098994369","https://openalex.org/W2100196653","https://openalex.org/W2103453943","https://openalex.org/W2105315497","https://openalex.org/W2108507302","https://openalex.org/W2109407861","https://openalex.org/W2110065044","https://openalex.org/W2110312780","https://openalex.org/W2114803986","https://openalex.org/W2115219137","https://openalex.org/W2125508747","https://openalex.org/W2126602684","https://openalex.org/W2133446381","https://openalex.org/W2134597218","https://openalex.org/W2135000328","https://openalex.org/W2137683543","https://openalex.org/W2140115103","https://openalex.org/W2141408320","https://openalex.org/W2144710927","https://openalex.org/W2146264532","https://openalex.org/W2147794131","https://openalex.org/W2148014281","https://openalex.org/W2155861118","https://openalex.org/W2160689765","https://openalex.org/W2160697532","https://openalex.org/W2166103265","https://openalex.org/W2168157737","https://openalex.org/W4301861531"],"related_works":["https://openalex.org/W2073661767","https://openalex.org/W2143211236","https://openalex.org/W2380185347","https://openalex.org/W2370034659","https://openalex.org/W2027133237","https://openalex.org/W2103777723","https://openalex.org/W2159636084","https://openalex.org/W2610941444","https://openalex.org/W2117168988","https://openalex.org/W2154430121"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1],"rate":[2],"of":[3,21,33,44,92,118,157,190],"mRNA":[4],"transcription":[5,9,103,191],"is":[6,55,70,79],"controlled":[7],"by":[8,102],"factors":[10,104,192],"that":[11,28,69,184],"bind":[12],"to":[13,51,81,88,128,133,193],"specific":[14],"DNA":[15,100,112,142,194],"motifs":[16],"in":[17,95,146,155,199],"promoter":[18],"regions":[19],"upstream":[20],"protein":[22],"coding":[23,53],"genes.":[24,159],"Recent":[25],"results":[26,163],"indicate":[27],"not":[29,126],"only":[30],"the":[31,42,52,90,185],"presence":[32],"a":[34,45,67,171],"motif":[35,38,46,77,93,119,123,148,176,206],"but":[36],"also":[37],"context":[39,78,94,131],"(for":[40],"example":[41],"orientation":[43,151],"or":[47],"its":[48],"location":[49,120,149],"relative":[50],"sequence)":[54],"important":[56],"for":[57,99,106,187],"gene":[58,83,109,135,200],"regulation.":[59,84],"RESULTS:":[60],"In":[61],"this":[62],"study":[63],"we":[64,114],"present":[65],"ContextFinder,":[66],"tool":[68],"specifically":[71],"aimed":[72],"at":[73],"identifying":[74],"cases":[75],"where":[76],"likely":[80],"affect":[82,134],"We":[85,160,182],"used":[86],"ContextFinder":[87],"examine":[89],"role":[91],"S.":[96],"cerevisiae":[97],"both":[98,147],"binding":[101,113,189],"and":[105,150,169,178,195],"effects":[107],"on":[108,166,205],"expression.":[110],"For":[111],"found":[115,170],"significant":[116],"patterns":[117],"bias,":[121],"whereas":[122],"orientations":[124],"did":[125],"seem":[127],"matter.":[129],"Motif":[130],"appears":[132],"expression":[136],"even":[137],"more":[138,153],"than":[139],"it":[140],"affects":[141],"binding,":[143],"as":[144],"biases":[145],"were":[152],"frequent":[154],"promoters":[156],"co-expressed":[158],"validated":[161],"our":[162],"against":[164],"data":[165],"nucleosome":[167,179],"positioning,":[168],"negative":[172],"correlation":[173],"between":[174],"preferred":[175],"locations":[177],"occupancy.":[180],"CONCLUSION:":[181],"conclude":[183],"requirement":[186],"stable":[188],"their":[196],"subsequent":[197],"function":[198],"regulation":[201],"can":[202],"impose":[203],"constraints":[204],"context.":[207]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
