ConTra v2 : a tool to identify transcription factor binding sites across species, update 2011
- Author
- Stefan Broos (UGent) , Paco Hulpiau (UGent) , Jeroen Galle (UGent) , Bart Hooghe (UGent) , Frans Van Roy (UGent) and Pieter De Bleser (UGent)
- Organization
- 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
- Keywords
- IDENTIFICATION, GENE-REGULATION, MICRORNAS, PROMOTER, EXPRESSION, INTRON, CELLS, RNAS
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-2003438
- MLA
- Broos, Stefan, et al. “ConTra v2 : A Tool to Identify Transcription Factor Binding Sites across Species, Update 2011.” NUCLEIC ACIDS RESEARCH, vol. 39, no. suppl. 2, 2011, pp. W74–78, doi:10.1093/nar/gkr355.
- 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. https://doi.org/10.1093/nar/gkr355
- Chicago author-date
- 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): W74–78. https://doi.org/10.1093/nar/gkr355.
- Chicago author-date (all authors)
- 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. doi:10.1093/nar/gkr355.
- 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):W74–8.
- IEEE
- [1]S. Broos, P. Hulpiau, J. Galle, B. Hooghe, F. Van Roy, and P. De Bleser, “ConTra v2 : a tool to identify transcription factor binding sites across species, update 2011,” NUCLEIC ACIDS RESEARCH, vol. 39, no. suppl. 2, pp. W74–W78, 2011.
@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}},
keywords = {{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}},
}
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