Nucleic Acids Research Advance Access originally published online on December 5, 2006
Nucleic Acids Research 2007 35(Database issue):D122-D126; doi:10.1093/nar/gkl879
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Nucleic Acids Research, 2007, Vol. 35, Database issue D122-D126
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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PReMod: a database of genome-wide mammalian cis-regulatory module predictions
McGill University and Genome Quebec Innovation Center 740 Dr Penfield, Montreal, Qc, Canada H3A 1A4 1 Institut de Recherches Cliniques de Montréal 110 Pine Avenue West, Montréal, Qc, Canada H2W 1R7 2 McGill Center for Bioinformatics. McGill University 3775 University Street, room #332. Montréal, Qc, Canada H3A 2B4
*To whom correspondence should be addressed. Tel: 514 398 5209; Fax: 514 398 3387; Email: blanchem{at}mcb.mcgill.ca
Received August 15, 2006. Revised October 10, 2006. Accepted October 11, 2006.
We describe PReMod, a new database of genome-wide cis-regulatory module (CRM) predictions for both the human and the mouse genomes. The prediction algorithm, described previously in Blanchette et al. (2006) Genome Res., 16, 656–668, exploits the fact that many known CRMs are made of clusters of phylogenetically conserved and repeated transcription factors (TF) binding sites. Contrary to other existing databases, PReMod is not restricted to modules located proximal to genes, but in fact mostly contains distal predicted CRMs (pCRMs). Through its web interface, PReMod allows users to (i) identify pCRMs around a gene of interest; (ii) identify pCRMs that have binding sites for a given TF (or a set of TFs) or (iii) download the entire dataset for local analyses. Queries can also be refined by filtering for specific chromosomal regions, for specific regions relative to genes or for the presence of CpG islands. The output includes information about the binding sites predicted within the selected pCRMs, and a graphical display of their distribution within the pCRMs. It also provides a visual depiction of the chromosomal context of the selected pCRMs in terms of neighboring pCRMs and genes, all of which are linked to the UCSC Genome Browser and the NCBI. PReMod: http://genomequebec.mcgill.ca/PReMod.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
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