title: Genome-wide promoter extraction and analysis in human, mouse, and rat.
abstract: Large-scale and high-throughput genomics research needs reliable and comprehensive genome-wide promoter annotation resources. We have conducted a systematic investigation on how to improve mammalian promoter prediction by incorporating both transcript and conservation information. This enabled us to build a better multispecies promoter annotation pipeline and hence to create CSHLmpd (Cold Spring Harbor Laboratory Mammalian Promoter Database) for the biomedical research community, which can act as a starting reference system for more refined functional annotations.
authors.affiliation: Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA. xuan@cshl.edu
authors.forename: Zhenyu
authors.initials: Z
authors.lastname: Xuan
authors.forename: Fang
authors.initials: F
authors.lastname: Zhao
authors.forename: Jinhua
authors.initials: J
authors.lastname: Wang
authors.forename: Gengxin
authors.initials: G
authors.lastname: Chen
authors.forename: Michael Q
authors.initials: MQ
authors.lastname: Zhang
mesh_terms: D000818:Animals; D017124:Conserved Sequence / Q000235:genetics; D018899:CpG Islands / Q000235:genetics; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D016678:Genome / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D051381:Rats; D012107:Research Design; D012680:Sensitivity and Specificity; D013045:Species Specificity; D014584:User-Computer Interface
chemical_list: D012333:RNA, Messenger