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ConTra v2: a tool to identify transcription factor binding sites across species, update 2011

Stefan Broos UGent, Paco Hulpiau UGent, Jeroen Galle UGent, Bart Hooghe UGent, Frans Van Roy UGent and Pieter De Bleser UGent (2011) NUCLEIC ACIDS RESEARCH. 39(suppl. 2). p.W74-W78
abstract
Transcription factors are important gene regulators with distinctive roles in development, cell signaling and cell cycling, and they have been associated with many diseases. The ConTra v2 web server allows easy visualization and exploration of predicted transcription factor binding sites in any genomic region surrounding coding or non-coding genes. In this new version, users can choose from nine reference organisms ranging from human to yeast. ConTra v2 can analyze promoter regions, 5'-UTRs, 3'-UTRs and introns or any other genomic region of interest. Hundreds of position weight matrices are available to choose from, but the user can also upload any other matrices for detecting specific binding sites. A typical analysis is run in four simple steps of choosing the gene, the transcript, the region of interest and then selecting one or more transcription factor binding sites. The ConTra v2 web server is freely available at http://bioit.dmbr.ugent.be/contrav2/index.php
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
IDENTIFICATION, GENE-REGULATION, MICRORNAS, PROMOTER, EXPRESSION, INTRON, CELLS, RNAS
journal title
NUCLEIC ACIDS RESEARCH
Nucleic Acids Res.
volume
39
issue
suppl. 2
pages
W74 - W78
Web of Science type
Article
Web of Science id
000292325300013
JCR category
BIOCHEMISTRY & MOLECULAR BIOLOGY
JCR impact factor
8.026 (2011)
JCR rank
26/286 (2011)
JCR quartile
1 (2011)
ISSN
0305-1048
DOI
10.1093/nar/gkr355
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
2003438
handle
http://hdl.handle.net/1854/LU-2003438
date created
2012-01-25 17:01:11
date last changed
2012-06-26 14:32:31
@article{2003438,
  abstract     = {Transcription factors are important gene regulators with distinctive roles in development, cell signaling and cell cycling, and they have been associated with many diseases. The ConTra v2 web server allows easy visualization and exploration of predicted transcription factor binding sites in any genomic region surrounding coding or non-coding genes. In this new version, users can choose from nine reference organisms ranging from human to yeast. ConTra v2 can analyze promoter regions, 5'-UTRs, 3'-UTRs and introns or any other genomic region of interest. Hundreds of position weight matrices are available to choose from, but the user can also upload any other matrices for detecting specific binding sites. A typical analysis is run in four simple steps of choosing the gene, the transcript, the region of interest and then selecting one or more transcription factor binding sites. The ConTra v2 web server is freely available at http://bioit.dmbr.ugent.be/contrav2/index.php},
  author       = {Broos, Stefan and Hulpiau, Paco and Galle, Jeroen and Hooghe, Bart and Van Roy, Frans and De Bleser, Pieter},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keyword      = {IDENTIFICATION,GENE-REGULATION,MICRORNAS,PROMOTER,EXPRESSION,INTRON,CELLS,RNAS},
  language     = {eng},
  number       = {suppl. 2},
  pages        = {W74--W78},
  title        = {ConTra v2: a tool to identify transcription factor binding sites across species, update 2011},
  url          = {http://dx.doi.org/10.1093/nar/gkr355},
  volume       = {39},
  year         = {2011},
}

Chicago
Broos, Stefan, Paco Hulpiau, Jeroen Galle, Bart Hooghe, Frans Van Roy, and Pieter De Bleser. 2011. “ConTra V2: a Tool to Identify Transcription Factor Binding Sites Across Species, Update 2011.” Nucleic Acids Research 39 (suppl. 2): W74–W78.
APA
Broos, S., Hulpiau, P., Galle, J., Hooghe, B., Van Roy, F., & De Bleser, P. (2011). ConTra v2: a tool to identify transcription factor binding sites across species, update 2011. NUCLEIC ACIDS RESEARCH, 39(suppl. 2), W74–W78.
Vancouver
1.
Broos S, Hulpiau P, Galle J, Hooghe B, Van Roy F, De Bleser P. ConTra v2: a tool to identify transcription factor binding sites across species, update 2011. NUCLEIC ACIDS RESEARCH. 2011;39(suppl. 2):W74–W78.
MLA
Broos, Stefan, Paco Hulpiau, Jeroen Galle, et al. “ConTra V2: a Tool to Identify Transcription Factor Binding Sites Across Species, Update 2011.” NUCLEIC ACIDS RESEARCH 39.suppl. 2 (2011): W74–W78. Print.