Sat, 05 Jul 2008 21:39:55 BST CiteULike: indigoviolet's Davis http://www.citeulike.org/user/indigoviolet/author/Davis CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/indigoviolet/article/212874 <i>Nat Genet, Vol. 25, No. 1. (May 2000), pp. 25-29.</i> Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. M Ashburner CA Ball JA Blake D Botstein H Butler JM Cherry AP Davis K Dolinski SS Dwight JT Eppig MA Harris DP Hill L Issel-Tarver A Kasarskis S Lewis JC Matese JE Richardson M Ringwald GM Rubin G Sherlock doi:10.1038/75556 Nat Genet, Vol. 25, No. 1. (May 2000), pp. 25-29. 2005-05-27T12:30:22-00:00 2000 Nat Genet 1061-4036 25 1 25 29 no-tag http://www.citeulike.org/user/indigoviolet/article/1074008 <i>Genome Res (8 January 2007)</i><br /><br />Recent studies suggest that surprisingly many mammalian genes have alternative promoters (APs); however, their biological roles, and the characteristics that distinguish them from single promoters (SPs), remain poorly understood. We constructed a large data set of evolutionarily conserved promoters, and used it to identify sequence features, functional associations, and expression patterns that differ by promoter type. The four promoter categories CpG-rich APs, CpG-poor APs, CpG-rich SPs, and CpG-poor SPs each show characteristic strengths and patterns of sequence conservation, frequencies of putative transcription-related motifs, and tissue and developmental stage expression preferences. APs display substantially higher sequence conservation than SPs and CpG-poor promoters than CpG-rich promoters. Among CpG-poor promoters, APs and SPs show sharply contrasting developmental stage preferences and TATA box frequencies. We developed a discriminator to computationally predict promoter type, verified its accuracy through experimental tests that incorporate a novel method for deconvolving mixed sequence traces, and used it to find several new APs. The discriminator predicts that almost half of all mammalian genes have evolutionarily conserved APs. This high frequency of APs, together with the strong purifying selection maintaining them, implies a crucial role in expanding the expression diversity of the mammalian genome. Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters. Daehyun Baek Colleen Davis Brent Ewing David Gordon Phil Green doi:10.1101/gr.5872707 Genome Res (8 January 2007) 2007-01-29T08:45:12-00:00 2007 Genome Res 1088-9051 no-tag