The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data

The Eukaryotic Promoter Database (EPD) is an annotated, non-redundant collection of eukaryotic Pol II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes a description of the initiation site mapping data, exhaustive cross-references to the EMBL nucleotide sequence database, SWISS-PROT, TRANSFAC and other databases, as well as bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. World Wide Web-based interfaces have been developed which enable the user to view EPD entries in different formats, to select and extract promoter sequences according to a variety of criteria, and to navigate to related databases exploiting different cross-references. The EPD web site also features yearly updated base frequency matrices for major eukaryotic promoter elements. EPD can be accessed at http://www.epd.isb-sib.ch.

[1]  P Bucher,et al.  Compilation and analysis of eukaryotic POL II promoter sequences. , 1986, Nucleic acids research.

[2]  T. Tsunoda,et al.  Identification and characterization of the potential promoter regions of 1031 kinds of human genes. , 2001, Genome research.

[3]  Alexander E. Kel,et al.  Transcription Regulatory Regions Database (TRRD): its status in 2000 , 2000, Nucleic Acids Res..

[4]  Xin Chen,et al.  TRANSFAC: an integrated system for gene expression regulation , 2000, Nucleic Acids Res..

[5]  Judith A. Blake,et al.  The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse , 2000, Nucleic Acids Res..

[6]  Philipp Bucher,et al.  The Eukaryotic Promoter Database (EPD): recent developments , 1999, Nucleic Acids Res..

[7]  Philipp Bucher,et al.  The Eukaryotic Promoter Database (EPD) , 2000, Nucleic Acids Res..

[8]  J. Fickett,et al.  Eukaryotic promoter recognition. , 1997, Genome research.

[9]  Andrey N. Naumochkin,et al.  Transcription Regulatory Regions Database (TRRD): its status in 2002 , 2002, Nucleic Acids Res..

[10]  P. Bucher.  Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. , 1990, Journal of molecular biology.

[11]  Yoshihiro Ugawa,et al.  Plant cis-acting regulatory DNA elements (PLACE) database: 1999 , 1999, Nucleic Acids Res..

[12]  Stephane Rombauts,et al.  PlantCARE, a plant cis-acting regulatory element database , 1999, Nucleic Acids Res..

[13]  A Suyama,et al.  Diverse transcriptional initiation revealed by fine, large‐scale mapping of mRNA start sites , 2001, EMBO reports.

[14]  Rodrigo Lopez,et al.  The EMBL Nucleotide Sequence Database , 1999, Nucleic Acids Res..

[15]  The FlyBase database of the Drosophila genome projects and community literature. , 2003, Nucleic acids research.

[16]  D. Valle,et al.  Online Mendelian Inheritance In Man (OMIM) , 2000, Human mutation.

[17]  Philipp Bucher,et al.  SEView: a Java applet for browsing molecular sequence data , 1998, Silico Biol..

[18]  Alexander E. Kel,et al.  Transcription Regulatory Regions Database (TRRD): its status in 1999 , 1999, Nucleic Acids Res..

[19]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 , 2000, Nucleic Acids Res..

[20]  P. Argos,et al.  SRS: information retrieval system for molecular biology data banks. , 1996, Methods in enzymology.

[21]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence data bank and its supplement TrEMBL , 1997, Nucleic Acids Res..

[22]  R D Klausner,et al.  The mammalian gene collection. , 1999, Science.

[23]  David Ghosh,et al.  Object oriented Transcription Factors Database (ooTFD) , 1999, Nucleic Acids Res..