{"id":"https://openalex.org/W2144893361","doi":"https://doi.org/10.1186/1471-2105-15-83","title":"Bioinformatics analysis of transcriptional regulation of circadian genes in rat liver","display_name":"Bioinformatics analysis of transcriptional regulation of circadian genes in rat liver","publication_year":2014,"publication_date":"2014-03-25","ids":{"openalex":"https://openalex.org/W2144893361","doi":"https://doi.org/10.1186/1471-2105-15-83","mag":"2144893361","pmid":"https://pubmed.ncbi.nlm.nih.gov/24666587"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-15-83","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-83","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-83","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/10.1186/1471-2105-15-83","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100642009","display_name":"Tung Nguyen","orcid":"https://orcid.org/0000-0003-4232-0566"},"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":"Tung T Nguyen","raw_affiliation_strings":["BioMaPS Institute for Quantitative Biology, Rutgers the State University of New Jersey, Piscataway, NJ, 08854, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioMaPS Institute for Quantitative Biology, Rutgers the State University of New Jersey, Piscataway, NJ, 08854, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103021108","display_name":"John Mattick","orcid":"https://orcid.org/0000-0002-8743-1158"},"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":"John SA Mattick","raw_affiliation_strings":["Chemical and Biochemical Engineering Department, Rutgers the State University of New Jersey, Piscataway, NJ, 08854, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chemical and Biochemical Engineering Department, Rutgers the State University of New Jersey, Piscataway, NJ, 08854, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101576454","display_name":"Qian Yang","orcid":"https://orcid.org/0000-0002-9493-6381"},"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":"Qian Yang","raw_affiliation_strings":["Chemical and Biochemical Engineering Department, Rutgers the State University of New Jersey, Piscataway, NJ, 08854, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chemical and Biochemical Engineering Department, Rutgers the State University of New Jersey, Piscataway, NJ, 08854, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075128403","display_name":"Mehmet A. Orman","orcid":"https://orcid.org/0000-0001-8499-9154"},"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":"Mehmet A Orman","raw_affiliation_strings":["Chemical and Biochemical Engineering Department, Rutgers the State University of New Jersey, Piscataway, NJ, 08854, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chemical and Biochemical Engineering Department, Rutgers the State University of New Jersey, Piscataway, NJ, 08854, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069724844","display_name":"Marianthi Ierapetritou","orcid":"https://orcid.org/0000-0002-1758-9777"},"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":"Marianthi G Ierapetritou","raw_affiliation_strings":["Chemical and Biochemical Engineering Department, Rutgers the State University of New Jersey, Piscataway, NJ, 08854, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chemical and Biochemical Engineering Department, Rutgers the State University of New Jersey, Piscataway, NJ, 08854, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086225019","display_name":"Fran\u00e7ois Berthiaume","orcid":"https://orcid.org/0000-0002-6914-4876"},"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":"Francois Berthiaume","raw_affiliation_strings":["Biomedical Engineering Department, Rutgers the State University of New Jersey, Piscataway, NJ, 08854, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Engineering Department, Rutgers the State University of New Jersey, Piscataway, NJ, 08854, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049184270","display_name":"Ioannis P. Androulakis","orcid":"https://orcid.org/0000-0002-3795-3628"},"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":"Ioannis P Androulakis","raw_affiliation_strings":["Chemical and Biochemical Engineering Department, Rutgers the State University of New Jersey, Piscataway, NJ 08854, USA. yannis@rci.rutgers.edu","Biomedical Engineering Department, Rutgers the State University of New Jersey, Piscataway, NJ, 08854, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chemical and Biochemical Engineering Department, Rutgers the State University of New Jersey, Piscataway, NJ 08854, USA. yannis@rci.rutgers.edu","institution_ids":["https://openalex.org/I102322142"]},{"raw_affiliation_string":"Biomedical Engineering Department, Rutgers the State University of New Jersey, Piscataway, NJ, 08854, USA","institution_ids":["https://openalex.org/I102322142"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5049184270"],"corresponding_institution_ids":["https://openalex.org/I102322142"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.1599,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.75384876,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"15","issue":"1","first_page":"83","last_page":"83"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10342","display_name":"Circadian rhythm and melatonin","score":0.9890999794006348,"subfield":{"id":"https://openalex.org/subfields/2807","display_name":"Endocrine and Autonomic Systems"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10342","display_name":"Circadian rhythm and melatonin","score":0.9890999794006348,"subfield":{"id":"https://openalex.org/subfields/2807","display_name":"Endocrine and Autonomic Systems"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.002400000113993883,"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/T10184","display_name":"Plant Molecular Biology Research","score":0.0008999999845400453,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.8220638036727905},{"id":"https://openalex.org/keywords/circadian-rhythm","display_name":"Circadian rhythm","score":0.7911324501037598},{"id":"https://openalex.org/keywords/circadian-clock","display_name":"Circadian clock","score":0.7223434448242188},{"id":"https://openalex.org/keywords/transcriptional-regulation","display_name":"Transcriptional regulation","score":0.5934063196182251},{"id":"https://openalex.org/keywords/regulator","display_name":"Regulator","score":0.5494831800460815},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5108823180198669},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.5077899098396301},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.47259005904197693},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.4585127830505371},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4432344436645508},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.41895946860313416},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.3536331057548523},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3447824716567993},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.20190203189849854}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8220638036727905},{"id":"https://openalex.org/C121446783","wikidata":"https://www.wikidata.org/wiki/Q208353","display_name":"Circadian rhythm","level":2,"score":0.7911324501037598},{"id":"https://openalex.org/C38606739","wikidata":"https://www.wikidata.org/wiki/Q5121352","display_name":"Circadian clock","level":3,"score":0.7223434448242188},{"id":"https://openalex.org/C27153228","wikidata":"https://www.wikidata.org/wiki/Q3787274","display_name":"Transcriptional regulation","level":4,"score":0.5934063196182251},{"id":"https://openalex.org/C6929976","wikidata":"https://www.wikidata.org/wiki/Q3771881","display_name":"Regulator","level":3,"score":0.5494831800460815},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5108823180198669},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.5077899098396301},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.47259005904197693},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4585127830505371},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4432344436645508},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.41895946860313416},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.3536331057548523},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3447824716567993},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.20190203189849854}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"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":"D002940","descriptor_name":"Circadian Rhythm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002940","descriptor_name":"Circadian Rhythm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002940","descriptor_name":"Circadian Rhythm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","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":"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":"D017207","descriptor_name":"Rats, Sprague-Dawley","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017207","descriptor_name":"Rats, Sprague-Dawley","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017207","descriptor_name":"Rats, Sprague-Dawley","qualifier_ui":null,"qualifier_name":null,"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":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056925","descriptor_name":"Circadian Rhythm Signaling Peptides and Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056925","descriptor_name":"Circadian Rhythm Signaling Peptides and Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056925","descriptor_name":"Circadian Rhythm Signaling Peptides and Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056925","descriptor_name":"Circadian Rhythm Signaling Peptides and Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D056925","descriptor_name":"Circadian Rhythm Signaling Peptides and Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D056925","descriptor_name":"Circadian Rhythm Signaling Peptides and Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-15-83","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-83","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-83","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:24666587","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24666587","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:alma.01RUT_INST:11663375360004646","is_oa":false,"landing_page_url":"https://scholarship.libraries.rutgers.edu/esploro/outputs/journalArticle/Bioinformatics-analysis-of-transcriptional-regulation-of/991031653880804646","pdf_url":null,"source":{"id":"https://openalex.org/S4210197018","display_name":"View","issn_l":"2688-268X","issn":["2688-268X","2688-3988"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:europepmc.org:2984170","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3987685","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3987685","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3987685","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"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-15-83","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-83","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-83","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":[{"id":"https://openalex.org/G4477642781","display_name":null,"funder_award_id":"GM082974","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"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":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2144893361.pdf","grobid_xml":"https://content.openalex.org/works/W2144893361.grobid-xml"},"referenced_works_count":79,"referenced_works":["https://openalex.org/W57243106","https://openalex.org/W953943906","https://openalex.org/W1537971445","https://openalex.org/W1550534049","https://openalex.org/W1579390242","https://openalex.org/W1939038991","https://openalex.org/W1964504813","https://openalex.org/W1971839242","https://openalex.org/W1978856373","https://openalex.org/W1982988226","https://openalex.org/W1983426369","https://openalex.org/W1983630187","https://openalex.org/W1984912966","https://openalex.org/W1986014242","https://openalex.org/W1986599980","https://openalex.org/W1989359395","https://openalex.org/W1991298209","https://openalex.org/W1992669445","https://openalex.org/W1993983731","https://openalex.org/W1998448534","https://openalex.org/W2002488861","https://openalex.org/W2011874680","https://openalex.org/W2012549433","https://openalex.org/W2015769702","https://openalex.org/W2022984362","https://openalex.org/W2024493318","https://openalex.org/W2026520695","https://openalex.org/W2026930722","https://openalex.org/W2030685718","https://openalex.org/W2035406373","https://openalex.org/W2038437697","https://openalex.org/W2041041851","https://openalex.org/W2043032255","https://openalex.org/W2045441934","https://openalex.org/W2048324184","https://openalex.org/W2055170554","https://openalex.org/W2058080431","https://openalex.org/W2059359814","https://openalex.org/W2059550141","https://openalex.org/W2060212825","https://openalex.org/W2060925737","https://openalex.org/W2068412840","https://openalex.org/W2070336334","https://openalex.org/W2071933658","https://openalex.org/W2080498142","https://openalex.org/W2085483223","https://openalex.org/W2086914764","https://openalex.org/W2087802228","https://openalex.org/W2090209293","https://openalex.org/W2095042100","https://openalex.org/W2099496913","https://openalex.org/W2101600063","https://openalex.org/W2104168874","https://openalex.org/W2106049005","https://openalex.org/W2109487010","https://openalex.org/W2115583552","https://openalex.org/W2116087472","https://openalex.org/W2122135124","https://openalex.org/W2123789196","https://openalex.org/W2123981584","https://openalex.org/W2125905177","https://openalex.org/W2126618928","https://openalex.org/W2127282382","https://openalex.org/W2130064388","https://openalex.org/W2133027051","https://openalex.org/W2141969791","https://openalex.org/W2150076905","https://openalex.org/W2153550523","https://openalex.org/W2154514232","https://openalex.org/W2156525687","https://openalex.org/W2157481078","https://openalex.org/W2159614898","https://openalex.org/W2160697532","https://openalex.org/W2161470536","https://openalex.org/W2164696529","https://openalex.org/W2170038164","https://openalex.org/W2337785247","https://openalex.org/W2440400476","https://openalex.org/W2997000181"],"related_works":["https://openalex.org/W2140682486","https://openalex.org/W4285097245","https://openalex.org/W2090209293","https://openalex.org/W3136837454","https://openalex.org/W2086660440","https://openalex.org/W2998298358","https://openalex.org/W2222265074","https://openalex.org/W2978063875","https://openalex.org/W2912720016","https://openalex.org/W2079326238"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1],"circadian":[2,34,43,60,132,220,227],"clock":[3,198],"is":[4,20,38],"a":[5,47,66,84,131,216],"critical":[6],"regulator":[7,23],"of":[8,24,33,86,123,197,205,229],"biological":[9],"functions":[10,231],"controlling":[11],"behavioral,":[12],"physiological":[13],"and":[14,30,112,119,145,175,183,242],"biochemical":[15],"processes.":[16],"Because":[17],"the":[18,21,27,31,55,63,91,135,187,233],"liver":[19,37,52,64],"primary":[22],"metabolites":[25],"within":[26,62,232],"mammalian":[28],"body":[29],"disruption":[32],"rhythms":[35],"in":[36,50,80,130],"associated":[39],"with":[40],"severe":[41],"illness,":[42],"regulators":[44,204],"would":[45],"play":[46],"strong":[48],"role":[49],"maintaining":[51],"function.":[53],"However,":[54],"regulatory":[56,217],"structure":[57,218],"that":[58,137,141,200],"governs":[59],"dynamics":[61,79,126],"at":[65],"transcriptional":[67,78,203],"level":[68],"remains":[69],"unknown.":[70],"To":[71],"explore":[72],"this":[73],"aspect,":[74],"we":[75,101,160,192,211],"analyzed":[76],"hepatic":[77],"Sprague-Dawley":[81],"rats":[82],"over":[83],"period":[85],"24":[87],"hours":[88],"to":[89,109,156,163,167,186,214,248],"assess":[90],"genome-wide":[92],"responses.":[93],"RESULTS:":[94],"Using":[95],"an":[96],"unsupervised":[97],"consensus":[98],"clustering":[99],"method,":[100],"identified":[102,194],"four":[103],"major":[104],"gene":[105,206],"expression":[106],"clusters,":[107],"corresponding":[108],"central":[110],"carbon":[111],"nitrogen":[113],"metabolism,":[114],"membrane":[115],"integrity,":[116],"immune":[117],"function,":[118],"DNA":[120],"repair,":[121],"all":[122],"which":[124,127,222,245],"have":[125],"suggest":[128],"regulation":[129,221],"manner.":[133],"With":[134],"assumption":[136],"transcription":[138],"factors":[139],"(TFs)":[140],"are":[142,154,180,201,246],"differentially":[143],"expressed":[144],"contain":[146],"CLOCK:BMAL1":[147],"binding":[148],"sites":[149],"on":[150],"their":[151],"proximal":[152],"promoters":[153],"likely":[155],"be":[157],"clock-controlled":[158,171],"TFs,":[159],"were":[161,212],"able":[162,213,247],"use":[164],"promoter":[165],"analysis":[166],"putatively":[168],"identify":[169],"additional":[170],"TFs":[172,179,199],"besides":[173],"PARF":[174],"RORA":[176],"families.":[177],"These":[178],"both":[181],"functionally":[182],"temporally":[184],"related":[185],"clusters":[188],"they":[189],"regulate.":[190],"Furthermore,":[191],"also":[193],"significant":[195],"sets":[196],"potentially":[202],"clusters.":[207],"CONCLUSIONS:":[208],"All":[209],"together,":[210],"propose":[215],"for":[219,226,250],"represents":[223],"alternative":[224],"paths":[225],"control":[228],"different":[230],"liver.":[234],"Our":[235],"prediction":[236],"has":[237],"been":[238],"affirmed":[239],"by":[240],"functional":[241],"temporal":[243],"analyses":[244],"extend":[249],"similar":[251],"studies.":[252]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":2}],"updated_date":"2026-06-23T13:55:30.953635","created_date":"2025-10-10T00:00:00"}