{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,9]],"date-time":"2024-08-09T21:11:30Z","timestamp":1723237890022},"reference-count":22,"publisher":"Springer Science and Business Media LLC","issue":"S4","license":[{"start":{"date-parts":[[2006,12,1]],"date-time":"2006-12-01T00:00:00Z","timestamp":1164931200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2006,12]]},"DOI":"10.1186\/1471-2105-7-s4-s2","type":"journal-article","created":{"date-parts":[[2006,12,12]],"date-time":"2006-12-12T19:59:21Z","timestamp":1165953561000},"source":"Crossref","is-referenced-by-count":20,"title":["Frequency distribution of TATA Box and extension sequences on human promoters"],"prefix":"10.1186","volume":"7","author":[{"given":"Wei","family":"Shi","sequence":"first","affiliation":[]},{"given":"Wanlei","family":"Zhou","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2006,12,12]]},"reference":[{"key":"1325_CR1","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1038\/nature03441","volume":"434","author":"X Xie","year":"2005","unstructured":"Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M: Systematic Discovery of Regulatory Motifs in Human Promoters and 30 UTRs by Comparison of Several Mammals. Nature 2005, 434: 338\u2013345. 10.1038\/nature03441","journal-title":"Nature"},{"key":"1325_CR2","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1126\/science.8211139","volume":"262","author":"CE Lawrence","year":"1993","unstructured":"Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC: Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment. Science 1993, 262: 208\u2013214. 10.1126\/science.8211139","journal-title":"Science"},{"key":"1325_CR3","first-page":"1","volume-title":"Genome Research","author":"PC FitzGerald","year":"2004","unstructured":"FitzGerald PC, Shlyakhtenko A, Mir AA, Vinson C: Clustering of DNA Sequences in Human Promoters. Genome Research 2004, 1\u201313."},{"key":"1325_CR4","doi-asserted-by":"publisher","first-page":"827","DOI":"10.1006\/jmbi.1998.1947","volume":"281","author":"JV Helden","year":"1998","unstructured":"Helden JV, Andre B, Collado-Vides J: Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. Journal of Molecular Biology 1998, 281: 827\u2013842. 10.1006\/jmbi.1998.1947","journal-title":"Journal of Molecular Biology"},{"key":"1325_CR5","doi-asserted-by":"publisher","first-page":"2553","DOI":"10.1093\/bioinformatics\/bth282","volume":"20","author":"MG Tadesse","year":"2004","unstructured":"Tadesse MG, Vannucci M, Lio P: Identification of DNA Regulatory Motifs Using Bayesian Variable Selection. Bioinformatics 2004, 20: 2553\u20132561. 10.1093\/bioinformatics\/bth282","journal-title":"Bioinformatics"},{"key":"1325_CR6","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1146\/annurev.biochem.72.121801.161520","volume":"72","author":"ST Smale","year":"2003","unstructured":"Smale ST, Kadonaga JT: The RNA Polymerase II Core Promoter. Annu Rev Biochem 2003, 72: 449\u201379. 10.1146\/annurev.biochem.72.121801.161520","journal-title":"Annu Rev Biochem"},{"key":"1325_CR7","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1152\/physiolgenomics.00040.2001","volume":"7","author":"LL Hsiao","year":"2001","unstructured":"Hsiao LL: A Compendium of Gene Expression in Normal Human Tissues. Physiological Genomics 2001, 7: 97\u2013104.","journal-title":"Physiological Genomics"},{"key":"1325_CR8","doi-asserted-by":"publisher","first-page":"362","DOI":"10.1016\/S0168-9525(03)00140-9","volume":"19","author":"E Eisenberg","year":"2003","unstructured":"Eisenberg E, Levanon EY: Human housekeeping genes are compact. Trends Genet 2003, 19: 362\u2013365. 10.1016\/S0168-9525(03)00140-9","journal-title":"Trends Genet"},{"key":"1325_CR9","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1152\/physiolgenomics.2000.2.3.143","volume":"2","author":"JA Warrington","year":"2000","unstructured":"Warrington JA, Nair A, MAHADEVAPPA M, Tsyganskaya M: Comparison of Human Adult and Fetal Expression and Identification of 535 Housekeeping\/Maintenance Genes. Physiological Genomics 2000, 2: 143\u2013147.","journal-title":"Physiological Genomics"},{"key":"1325_CR10","doi-asserted-by":"publisher","first-page":"1027","DOI":"10.1016\/j.cell.2004.11.040","volume":"119","author":"S Dorus","year":"2004","unstructured":"Dorus S: Accelerated Evolution of Nervous System Genes in the Origin of Homo Sapiens. Cell 2004, 119: 1027\u20131040. 10.1016\/j.cell.2004.11.040","journal-title":"Cell"},{"key":"1325_CR11","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1186\/1471-2164-6-25","volume":"6","author":"M Molina","year":"2005","unstructured":"Molina M, Grotewold E: Genome Wide Analysis of Arabidopsis Core Promotes. BMC Genomics 2005, 6: 25. 10.1186\/1471-2164-6-25","journal-title":"BMC Genomics"},{"key":"1325_CR12","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1006\/jmbi.1996.0456","volume":"261","author":"ZS Juo","year":"1996","unstructured":"Juo ZS, Chiu TK, Leiberman PM, Baikalov I, Berk AJ, Dickerson RE: How Proteins Recognize the TATA Box. J Mol Biol 1996, 261: 239\u2013254. 10.1006\/jmbi.1996.0456","journal-title":"J Mol Biol"},{"key":"1325_CR13","doi-asserted-by":"publisher","first-page":"677","DOI":"10.1101\/gr.GR-1640R","volume":"11","author":"Y Suzuki","year":"2001","unstructured":"Suzuki Y, Tsunoda T, Sese J, Taira H, Mizushima-Sugano J: Identification and Characterization of the Potential Promoter Regions of 1031 Kinds of Human genes. Genome Research 2001, 11: 677\u201384. 10.1101\/gr.GR-1640R","journal-title":"Genome Research"},{"key":"1325_CR14","doi-asserted-by":"publisher","first-page":"1890","DOI":"10.1093\/nar\/22.10.1890","volume":"22","author":"J Wong","year":"1994","unstructured":"Wong J, Bateman E: TBP-DNA Interactions in the Minor Groove Discriminate between A:T and T:A Base Pairs. Nucleic Acids Res 1994, 22: 1890\u201396.","journal-title":"Nucleic Acids Res"},{"key":"1325_CR15","doi-asserted-by":"publisher","first-page":"520","DOI":"10.1038\/365520a0","volume":"365","author":"JL Kim","year":"1993","unstructured":"Kim JL, Nikolov DB, Burley SK: Co-crystal Structure of TBP Recognizing the Minor Groove of a TATA Element. Nature 1993, 365: 520\u201327. 10.1038\/365520a0","journal-title":"Nature"},{"key":"1325_CR16","doi-asserted-by":"publisher","first-page":"512","DOI":"10.1038\/365512a0","volume":"365","author":"YC Kim","year":"1993","unstructured":"Kim YC, Geiger JH, Hahn S, Sigler PB: Crystal Structure of a Yeast TBP\/TATA-box Complex. Nature 1993, 365: 512\u201320. 10.1038\/365512a0","journal-title":"Nature"},{"key":"1325_CR17","doi-asserted-by":"publisher","first-page":"6699","DOI":"10.1093\/nar\/19.24.6699","volume":"19","author":"L Xu","year":"1991","unstructured":"Xu L, Thali M, Schaffner W: Upsteam Box\/TATA Box Order Is the Major Determinant of the Direction of Transcription. Nucleic Acids Res 1991, 19: 6699\u2013704.","journal-title":"Nucleic Acids Res"},{"key":"1325_CR18","doi-asserted-by":"crossref","first-page":"1391","DOI":"10.1016\/S0021-9258(18)48443-8","volume":"267","author":"A O'Shea-Greenfield","year":"1992","unstructured":"O'Shea-Greenfield A, Smale ST: Roles of TATA and initiator Elements in Determining the Start Site Location and Direction of RNA Polymerase II Transcription. J Biol Chem 1992, 267: 1391\u2013402.","journal-title":"J Biol Chem"},{"key":"1325_CR19","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1016\/0022-2836(90)90223-9","volume":"212","author":"P Bucher","year":"1990","unstructured":"Bucher P: Weight Matrix Descriptions of Four Eukaryotic RNA Polymerase II Promoter Elements Derived from 502 Unrelated Promoter Sequences. J Mol Biol 1990, 212: 563\u2013568. 10.1016\/0022-2836(90)90223-9","journal-title":"J Mol Biol"},{"key":"1325_CR20","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1159\/000068542","volume":"98","author":"C Martins","year":"2002","unstructured":"Martins C, Wasko AP, Oliveira C, Porto-Foresti F, Parise-Maltempi PP, Wright JM, Foresti F: Dynamics of 5S Rdna in the Tilapia(Oreochromis niloticus) genome: repeat units, inverted sequences, pseudogenes and chromosome loci. Cytogenet Genome Res 2002, 98: 78\u201385. 10.1159\/000068542","journal-title":"Cytogenet Genome Res"},{"key":"1325_CR21","doi-asserted-by":"publisher","first-page":"15664","DOI":"10.1074\/jbc.270.26.15664","volume":"270","author":"S Takeda","year":"1995","unstructured":"Takeda S, North DL, Diagana T, Miyagoe Y, Lakich MM, Whalen RG: Myogenic Regulatory Factors Can Activate TATA-containing Promoter Elements via an E-box Independent Mechanism. J Biol Chem 1995, 270: 15664\u201315670. 10.1074\/jbc.270.26.15664","journal-title":"J Biol Chem"},{"key":"1325_CR22","volume-title":"R: A Language and Environment for Statistical Computing","author":"R Development Core Team","year":"2006","unstructured":"R Development Core Team: R: A Language and Environment for Statistical Computing.R Foundation for Statistical Computing, Vienna, Austria; 2006. [ http:\/\/www.R-project.org ]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-7-S4-S2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-7-S4-S2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-7-S4-S2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,5]],"date-time":"2021-08-05T21:30:33Z","timestamp":1628199033000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-7-S4-S2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,12]]},"references-count":22,"journal-issue":{"issue":"S4","published-print":{"date-parts":[[2006,12]]}},"alternative-id":["1325"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-7-s4-s2","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006,12]]},"article-number":"S2"}}