We found a match
Your institution may have access to this item. Find your institution then sign in to continue.
- Title
Identifying synonymous regulatory elements in vertebrate genomes.
- Authors
Ovcharenko, Ivan; Nobrega, Marcelo A
- Abstract
Synonymous gene regulation, defined by regulatory elements driving shared temporal and/or spatial aspects of gene expression, is most probably predicated on genomic elements that contain similar modules of certain transcription factor binding sites (TFBS). We have developed a method to scan vertebrate genomes for evolutionary conserved modules of TFBS in a predefined configuration, and created a tool, named SynoR that identifies synonymous regulatory elements (SREs) in vertebrate genomes. SynoR performs de novo identification of SREs utilizing known patterns of TFBS in active regulatory elements (REs) as seeds for genome scans. Layers of multiple-species conservation allow the use of differential phylogenetic sequence conservation filters in search of SREs and the results are displayed such as to provide an extensive annotation of the genes containing the detected REs. Gene Ontology categories are utilized to further functionally classify the identified genes, and integrated GNF Expression Atlas 2 data allow the cataloging of tissue-specificities of the predicted SREs. SynoR is publicly available at http://synor.dcode.org.
- Publication
Nucleic acids research, 2005, Vol 33, Issue Web Server issue, pW403
- ISSN
1362-4962
- Publication type
Journal Article
- DOI
10.1093/nar/gki466