Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (62K) Freely available
Right arrow Supplementary Data
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (63)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Praz, V.
Right arrow Articles by Bucher, P.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Praz, V.
Right arrow Articles by Bucher, P.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2002, Vol. 30, No. 1 322-324
© 2002 Oxford University Press

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

Viviane Praz, Rouaïda Périer, Claude Bonnard and Philipp Bucher*

Swiss Institute of Bioinformatics and Swiss Institute for Experimental Cancer Research, Ch. des Boveresses 155, 1066-Epalinges s/Lausanne, Switzerland

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.

* To whom correspondence should be addressed. Tel: +41 21 692 5892; Fax: +41 21 692 5945; Email:philipp.bucher{at}isb-sib.ch


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
B. Jiang, M. Q. Zhang, and X. Zhang
OSCAR: One-class SVM for accurate recognition of cis-elements
Bioinformatics, November 1, 2007; 23(21): 2823 - 2828.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
J. J. Stewart, J. A. Fischbeck, X. Chen, and L. A. Stargell
Non-optimal TATA Elements Exhibit Diverse Mechanistic Consequences
J. Biol. Chem., August 11, 2006; 281(32): 22665 - 22673.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
S. J. Cooper, N. D. Trinklein, E. D. Anton, L. Nguyen, and R. M. Myers
Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome
Genome Res., January 1, 2006; 16(1): 1 - 10.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. D. Schmid, R. Perier, V. Praz, and P. Bucher
EPD in its twentieth year: towards complete promoter coverage of selected model organisms
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D82 - D85.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. Yamashita, Y. Suzuki, H. Wakaguri, K. Tsuritani, K. Nakai, and S. Sugano
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D86 - D89.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. Sun, S. K. Palaniswamy, T. T. Pohar, V. X. Jin, T. H.-M. Huang, and R. V. Davuluri
MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D98 - D103.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. D. Wren, W. H. Hildebrand, S. Chandrasekaran, and U. Melcher
Markov model recognition and classification of DNA/protein sequences within large text databases
Bioinformatics, November 1, 2005; 21(21): 4046 - 4053.
[Abstract] [Full Text] [PDF]

Home page
 ANN BOT (LOND)Home page
B. MOHANTY, S. P. T. KRISHNAN, S. SWARUP, and V. B. BAJIC
Detection and Preliminary Analysis of Motifs in Promoters of Anaerobically Induced Genes of Different Plant Species
Ann. Bot., September 1, 2005; 96(4): 669 - 681.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Kanhere and M. Bansal
Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes
Nucleic Acids Res., June 6, 2005; 33(10): 3165 - 3175.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. I. Gershenzon, G. D. Stormo, and I. P. Ioshikhes
Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites
Nucleic Acids Res., April 22, 2005; 33(7): 2290 - 2301.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Endocrinol.Home page
A. Sandelin and W. W. Wasserman
Prediction of Nuclear Hormone Receptor Response Elements
Mol. Endocrinol., March 1, 2005; 19(3): 595 - 606.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. Biol.Home page
M. M. Robinson, G. Yatherajam, R. T. Ranallo, A. Bric, M. R. Paule, and L. A. Stargell
Mapping and Functional Characterization of the TAF11 Interaction with TFIIA
Mol. Cell. Biol., February 1, 2005; 25(3): 945 - 957.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
Y. Suzuki, R. Yamashita, M. Shirota, Y. Sakakibara, J. Chiba, J. Mizushima-Sugano, K. Nakai, and S. Sugano
Sequence Comparison of Human and Mouse Genes Reveals a Homologous Block Structure in the Promoter Regions
Genome Res., September 1, 2004; 14(9): 1711 - 1718.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
M. H. Kohn, S. Fang, and C.-I Wu
Inference of Positive and Negative Selection on the 5' Regulatory Regions of Drosophila Genes
Mol. Biol. Evol., February 1, 2004; 21(2): 374 - 383.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
V. J. Makeev, A. P. Lifanov, A. G. Nazina, and D. A. Papatsenko
Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information
Nucleic Acids Res., October 15, 2003; 31(20): 6016 - 6026.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
B. Hoogendoorn, S. L. Coleman, C. A. Guy, K. Smith, T. Bowen, P. R. Buckland, and M. C. O'Donovan
Functional analysis of human promoter polymorphisms
Hum. Mol. Genet., September 15, 2003; 12(18): 2249 - 2254.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
G. A. Wray, M. W. Hahn, E. Abouheif, J. P. Balhoff, M. Pizer, M. V. Rockman, and L. A. Romano
The Evolution of Transcriptional Regulation in Eukaryotes
Mol. Biol. Evol., September 1, 2003; 20(9): 1377 - 1419.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. J. K. Edwards, T. J. Carver, T. Vavouri, M. Frith, M. J. Bishop, and G. Elgar
Theatre: a software tool for detailed comparative analysis and visualization of genomic sequence
Nucleic Acids Res., July 1, 2003; 31(13): 3510 - 3517.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Chong, G. Zhang, and V. B. Bajic
FIE2: a program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes
Nucleic Acids Res., July 1, 2003; 31(13): 3546 - 3553.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. S. Halees, D. Leyfer, and Z. Weng
PromoSer: a large-scale mammalian promoter and transcription start site identification service
Nucleic Acids Res., July 1, 2003; 31(13): 3554 - 3559.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
V. B. Bajic, S. L. Tan, A. Chong, S. Tang, A. Strom, J.-A. Gustafsson, C.-Y. Lin, and E. T. Liu
Dragon ERE Finder version 2: a tool for accurate detection and analysis of estrogen response elements in vertebrate genomes
Nucleic Acids Res., July 1, 2003; 31(13): 3605 - 3607.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
G. Ambrosini, V. Praz, V. Jagannathan, and P. Bucher
Signal search analysis server
Nucleic Acids Res., July 1, 2003; 31(13): 3618 - 3620.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. Falquet, L. Bordoli, V. Ioannidis, M. Pagni, and C. V. Jongeneel
Swiss EMBnet node web server
Nucleic Acids Res., July 1, 2003; 31(13): 3782 - 3783.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
S. Khambata-Ford, Y. Liu, C. Gleason, M. Dickson, R. B. Altman, S. Batzoglou, and R. M. Myers
Identification of Promoter Regions in the Human Genome by Using a Retroviral Plasmid Library-Based Functional Reporter Gene Assay
Genome Res., July 1, 2003; 13(7): 1765 - 1774.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
S. Rombauts, K. Florquin, M. Lescot, K. Marchal, P. Rouze, and Y. Van de Peer
Computational Approaches to Identify Promoters and cis-Regulatory Elements in Plant Genomes
Plant Physiology, July 1, 2003; 132(3): 1162 - 1176.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
R. Elkon, C. Linhart, R. Sharan, R. Shamir, and Y. Shiloh
Genome-Wide In Silico Identification of Transcriptional Regulators Controlling the Cell Cycle in Human Cells
Genome Res., May 1, 2003; 13(5): 773 - 780.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
H. Guo and S. P. Moose
Conserved Noncoding Sequences among Cultivated Cereal Genomes Identify Candidate Regulatory Sequence Elements and Patterns of Promoter Evolution
PLANT CELL, May 1, 2003; 15(5): 1143 - 1158.
[Abstract] [Full Text]

Home page
 Nucleic Acids ResHome page
J. Zheng, J. Wu, and Z. Sun
An approach to identify over-represented cis-elements in related sequences
Nucleic Acids Res., April 1, 2003; 31(7): 1995 - 2005.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. Dieterich, H. Wang, K. Rateitschak, H. Luz, and M. Vingron
CORG: a database for COmparative Regulatory Genomics
Nucleic Acids Res., January 1, 2003; 31(1): 55 - 57.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
I. A. Shahmuradov, A. J. Gammerman, J. M. Hancock, P. M. Bramley, and V. V. Solovyev
PlantProm: a database of plant promoter sequences
Nucleic Acids Res., January 1, 2003; 31(1): 114 - 117.
[Abstract] [Full Text] [PDF]

Home page
 Genes Dev.Home page
M. Labrador and V. G. Corces
Phosphorylation of histone H3 during transcriptional activation depends on promoter structure
Genes & Dev., January 1, 2003; 17(1): 43 - 48.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
S. L. Coleman, P. R. Buckland, B. Hoogendoorn, C. Guy, K. Smith, and M. C. O'Donovan
Experimental analysis of the annotation of promoters in the public database
Hum. Mol. Genet., August 1, 2002; 11(16): 1817 - 1821.
[Abstract] [Full Text] [PDF]

Home page
 Endocr. Rev.Home page
C. P. Leo, S. Y. Hsu, and A. J. W. Hsueh
Hormonal Genomics
Endocr. Rev., June 1, 2002; 23(3): 369 - 381.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.