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Generic eukaryotic core promoter prediction using structural features of DNA

Thomas Abeel UGent, Yvan Saeys UGent, Eric Bonnet UGent, Pierre Rouzé UGent and Yves Van de Peer UGent (2008) GENOME RESEARCH. 18(2). p.310-323
abstract
Despite many recent efforts, in silico identification of promoter regions is still in its infancy. However, the accurate identification and delineation of promoter regions is important for several reasons, such as improving genome annotation and devising experiments to study and understand transcriptional regulation. Current methods to identify the core region of promoters require large amounts of high-quality training data and often behave like black box models that output predictions that are difficult to interpret. Here, we present a novel approach for predicting promoters in whole-genome sequences by using large-scale structural properties of DNA. Our technique requires no training, is applicable to many eukaryotic genomes, and performs extremely well in comparison with the best available promoter prediction programs. Moreover, it is fast, simple in design, and has no size constraints, and the results are easily interpretable. We compared our approach with 14 current state-of-the-art implementations using human gene and transcription start site data and analyzed the ENCODE region in more detail. We also validated our method on 12 additional eukaryotic genomes, including vertebrates, invertebrates, plants, fungi, and protists.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (review)
publication status
published
subject
keyword
POLYMERASE-II PROMOTERS, TRANSCRIPTION START SITES, TATA-BINDING PROTEIN, DISTINCTIVE MECHANICAL PROPERTY, GENOME-WIDE ANALYSIS, CPG ISLANDS, DROSOPHILA-MELANOGASTER, COMPREHENSIVE ANALYSIS, FLANKING SEQUENCES, PLANT GENOMES
journal title
GENOME RESEARCH
Genome Res.
volume
18
issue
2
pages
310 - 323
Web of Science type
Review
Web of Science id
000252860700014
JCR category
BIOTECHNOLOGY & APPLIED MICROBIOLOGY
JCR impact factor
10.176 (2008)
JCR rank
5/144 (2008)
JCR quartile
1 (2008)
ISSN
1088-9051
DOI
10.1101/gr.6991408
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
417320
handle
http://hdl.handle.net/1854/LU-417320
date created
2008-06-04 10:04:00
date last changed
2012-12-05 12:05:33
@article{417320,
  abstract     = {Despite many recent efforts, in silico identification of promoter regions is still in its infancy. However, the accurate identification and delineation of promoter regions is important for several reasons, such as improving genome annotation and devising experiments to study and understand transcriptional regulation. Current methods to identify the core region of promoters require large amounts of high-quality training data and often behave like black box models that output predictions that are difficult to interpret. Here, we present a novel approach for predicting promoters in whole-genome sequences by using large-scale structural properties of DNA. Our technique requires no training, is applicable to many eukaryotic genomes, and performs extremely well in comparison with the best available promoter prediction programs. Moreover, it is fast, simple in design, and has no size constraints, and the results are easily interpretable. We compared our approach with 14 current state-of-the-art implementations using human gene and transcription start site data and analyzed the ENCODE region in more detail. We also validated our method on 12 additional eukaryotic genomes, including vertebrates, invertebrates, plants, fungi, and protists.},
  author       = {Abeel, Thomas and Saeys, Yvan and Bonnet, Eric and Rouz{\'e}, Pierre and Van de Peer, Yves},
  issn         = {1088-9051},
  journal      = {GENOME RESEARCH},
  keyword      = {POLYMERASE-II PROMOTERS,TRANSCRIPTION START SITES,TATA-BINDING PROTEIN,DISTINCTIVE MECHANICAL PROPERTY,GENOME-WIDE ANALYSIS,CPG ISLANDS,DROSOPHILA-MELANOGASTER,COMPREHENSIVE ANALYSIS,FLANKING SEQUENCES,PLANT GENOMES},
  language     = {eng},
  number       = {2},
  pages        = {310--323},
  title        = {Generic eukaryotic core promoter prediction using structural features of DNA},
  url          = {http://dx.doi.org/10.1101/gr.6991408},
  volume       = {18},
  year         = {2008},
}

Chicago
Abeel, Thomas, Yvan Saeys, Eric Bonnet, Pierre Rouzé, and Yves Van de Peer. 2008. “Generic Eukaryotic Core Promoter Prediction Using Structural Features of DNA.” Genome Research 18 (2): 310–323.
APA
Abeel, T., Saeys, Y., Bonnet, E., Rouzé, P., & Van de Peer, Y. (2008). Generic eukaryotic core promoter prediction using structural features of DNA. GENOME RESEARCH, 18(2), 310–323.
Vancouver
1.
Abeel T, Saeys Y, Bonnet E, Rouzé P, Van de Peer Y. Generic eukaryotic core promoter prediction using structural features of DNA. GENOME RESEARCH. 2008;18(2):310–23.
MLA
Abeel, Thomas, Yvan Saeys, Eric Bonnet, et al. “Generic Eukaryotic Core Promoter Prediction Using Structural Features of DNA.” GENOME RESEARCH 18.2 (2008): 310–323. Print.