Skip Navigation


Bioinformatics Advance Access originally published online on April 26, 2005
Bioinformatics 2005 21(13):3058-3059; doi:10.1093/bioinformatics/bti461
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/13/3058    most recent
bti461v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
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 (7)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Donaldson, I. J.
Right arrow Articles by Göttgens, B.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Donaldson, I. J.
Right arrow Articles by Göttgens, B.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

TFBScluster: a resource for the characterization of transcriptional regulatory networks

Ian John Donaldson , Michael Chapman and Berthold Göttgens *

Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge Hills Road, Cambridge CB2 2XY, UK

*To whom correspondence should be addressed.

Summary: One major challenge of the post-sequencing era of the human genome project will be the functional annotation of the non-coding portion of the genome, in particular gene regulatory sequences. We have developed a new web-based tool, TFBScluster, which performs genome-wide identification of transcription factor binding site clusters that are conserved in multiple mammalian genomes. Clusters representing candidate gene regulatory elements can be filtered further, based on the presence or absence of additional user-defined DNA sequence motifs or by constraining the orientation or order of binding sites. Comprehensive results files, returned by email, are designed to facilitate experimental validation of computationally identified candidate gene regulatory sequences. TFBScluster, therefore, has the potential to contribute to deciphering transcriptional networks that regulate a wide range of mammalian developmental processes.

Availability: http://hscl.cimr.cam.ac.uk/TFBScluster_genome_34.html

Contact: bg200{at}cam.ac.uk

Supplementary information: http://hscl.cimr.cam.ac.uk/sup_don05_app_api.html


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
W. Fu, P. Ray, and E. P. Xing
DISCOVER: a feature-based discriminative method for motif search in complex genomes
Bioinformatics, June 15, 2009; 25(12): i321 - i329.
[Abstract] [Full Text] [PDF]

Home page
 BloodHome page
J.-R. Landry, N. Bonadies, S. Kinston, K. Knezevic, N. K. Wilson, S. H. Oram, M. Janes, S. Piltz, M. Hammett, J. Carter, et al.
Expression of the leukemia oncogene Lmo2 is controlled by an array of tissue-specific elements dispersed over 100 kb and bound by Tal1/Lmo2, Ets, and Gata factors
Blood, June 4, 2009; 113(23): 5783 - 5792.
[Abstract] [Full Text] [PDF]

Home page
 BloodHome page
N. K. Wilson, D. Miranda-Saavedra, S. Kinston, N. Bonadies, S. D. Foster, F. Calero-Nieto, M. A. Dawson, I. J. Donaldson, S. Dumon, J. Frampton, et al.
The transcriptional program controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic hematopoietic development
Blood, May 28, 2009; 113(22): 5456 - 5465.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
A. M. Smith, M.-J. Sanchez, G. A. Follows, S. Kinston, I. J. Donaldson, A. R. Green, and B. Gottgens
A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity
Genome Res., September 1, 2008; 18(9): 1422 - 1432.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. E. Pimanda, I. J. Donaldson, M. F. T. R. de Bruijn, S. Kinston, K. Knezevic, L. Huckle, S. Piltz, J.-R. Landry, A. R. Green, D. Tannahill, et al.
The SCL transcriptional network and BMP signaling pathway interact to regulate RUNX1 activity
PNAS, January 16, 2007; 104(3): 840 - 845.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
I. J. Donaldson and B. Gottgens
CoMoDis: composite motif discovery in mammalian genomes
Nucleic Acids Res., January 12, 2007; 35(1): e1 - e1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
I. J. Donaldson and B. Gottgens
TFBScluster web server for the identification of mammalian composite regulatory elements.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W524 - W528.
[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.