{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T17:08:10Z","timestamp":1776272890532,"version":"3.50.1"},"reference-count":22,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2008,10,10]],"date-time":"2008-10-10T00:00:00Z","timestamp":1223596800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000193","type":"journal-article","created":{"date-parts":[[2008,10,9]],"date-time":"2008-10-09T17:09:53Z","timestamp":1223572193000},"page":"e1000193","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":238,"title":["Analysis of Gene Regulatory Networks in the Mammalian Circadian Rhythm"],"prefix":"10.1371","volume":"4","author":[{"given":"Jun","family":"Yan","sequence":"first","affiliation":[]},{"given":"Haifang","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Yuting","family":"Liu","sequence":"additional","affiliation":[]},{"given":"Chunxuan","family":"Shao","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2008,10,10]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1146\/annurev.physiol.63.1.647","article-title":"Molecular analysis of mammalian circadian rhythms.","volume":"63","author":"SM Reppert","year":"2001","journal-title":"Annu Rev Physiol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1038\/nature00906","article-title":"A transcription factor response element for gene expression during circadian night.","volume":"418","author":"HR Ueda","year":"2002","journal-title":"Nature"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/S0092-8674(02)00722-5","article-title":"Coordinated transcription of key pathways in the mouse by the circadian clock.","volume":"109","author":"S Panda","year":"2002","journal-title":"Cell"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"3342","DOI":"10.1073\/pnas.0611724104","article-title":"Circadian and CLOCK-controlled regulation of the mouse transcriptome and cell proliferation.","volume":"104","author":"BH Miller","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1038\/ng1504","article-title":"System-level identification of transcriptional circuits underlying mammalian circadian clocks.","volume":"37","author":"HR Ueda","year":"2005","journal-title":"Nat Genet"},{"key":"ref6","first-page":"65","article-title":"Promoter analysis of mammalian clock controlled genes.","volume":"18","author":"K Bozek","year":"2007","journal-title":"Genome Inform"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"6062","DOI":"10.1073\/pnas.0400782101","article-title":"A gene atlas of the mouse and human protein-encoding transcriptomes.","volume":"101","author":"AI Su","year":"2004","journal-title":"Proc Natl Acad Sci"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1080\/07420520701800736","article-title":"Expression of clock genes in human peripheral blood mononuclear cells throughout the sleep\/wake and circadian cycles.","volume":"24","author":"FO James","year":"2007","journal-title":"Chronobiol Int"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1186\/1471-2105-6-168","article-title":"High-Throughput GoMiner, an \u2018industrial-strength\u2019 integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID).","volume":"6","author":"BR Zeeberg","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1186\/1471-2202-8-98","article-title":"Identification of novel light-induced genes in the suprachiasmatic nucleus.","volume":"8","author":"V Porterfield","year":"2007","journal-title":"BMC Neuroscience"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"1002","DOI":"10.1126\/science.1121613","article-title":"Nuclear receptor Rev-erb\u03b1 is a critical lithium-sensitive component of the circadian clock.","volume":"311","author":"L Yin","year":"2006","journal-title":"Science"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"e34","DOI":"10.1371\/journal.pbio.0050034","article-title":"System-driven and oscillator-dependent circadian transcription in mice with a conditionally active liver clock.","volume":"5","author":"B Kornmann","year":"2007","journal-title":"PLoS Biology"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1093\/nar\/30.1.328","article-title":"DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs.","volume":"30","author":"Y Suzuki","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"D97","DOI":"10.1093\/nar\/gkm901","article-title":"DBTSS: database of transcription start sites, progress report 2008.","volume":"36","author":"H Wakaguri","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1559","DOI":"10.1126\/science.1112014","article-title":"The transcriptional landscape of the mammalian genome.","volume":"309","author":"P Carninci","year":"2005","journal-title":"Science"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"D61","DOI":"10.1093\/nar\/gkl842","article-title":"NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.","volume":"35","author":"KD Pruitt","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"3576","DOI":"10.1093\/nar\/gkg585","article-title":"MATCH: A tool for searching transcription factor binding sites in DNA sequences.","volume":"31","author":"AE Kel","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"1753","DOI":"10.1093\/nar\/gkg268","article-title":"Toucan: deciphering the cis-regulatory logic of coregulated genes.","volume":"31","author":"S Aerts","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"Article7","DOI":"10.2202\/1544-6115.1032","article-title":"On the power of profiles for transcription factor binding site detection.","volume":"2","author":"S Rahmann","year":"2003","journal-title":"Stat Appl Genet Mol Biol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1093\/bioinformatics\/17.12.1113","article-title":"A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling.","volume":"17","author":"G Thijs","year":"2001","journal-title":"Bioinformatics"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1093\/bioinformatics\/15.7.563","article-title":"Identifying DNA and protein patterns with statistically significant alignments of multiple sequences.","volume":"15","author":"GZ Hertz","year":"1999","journal-title":"Bioinformatics"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"26839","DOI":"10.1155\/2007\/26839","article-title":"Comprehensive analysis of PPAR\u03b1-dependent regulation of hepatic lipid metabolism by expression profiling.","volume":"2007","author":"M Rakhshandehroo","year":"2007","journal-title":"PPAR Res"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000193","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,14]],"date-time":"2019-05-14T10:30:56Z","timestamp":1557829856000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000193"}},"subtitle":[],"editor":[{"given":"Jeffrey M.","family":"Gimble","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2008,10,10]]},"references-count":22,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2008,10,10]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000193","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,10,10]]}}}