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A Concept for ab initio Prediction of cis-regulatory Modules.
MedLine Citation:
PMID:  22430433     Owner:  NLM     Status:  In-Data-Review    
Abstract/OtherAbstract:
An important concern in the attempt of understanding the functional code of eukaryotic genes is to elucidate the control structures for regulating gene activation and suppression. One objective in the attempt to understand mechanisms of gene regulation is the elucidation of the regulatory network structure. A preliminary step of a detailed network analysis is identifying the transcription factor binding sites of a regulatory network. Known as cis-regulatory module (CRM), it is understood as part of the genome that comprises a set of short length binding sites. Gene regulatory systems are known to be quite stable during evolution, as compared to relatively frequent replication processes of genes and mutations of the coding sequences. This conservation property of regulatory code can advantageously be used for identifying cis-regulatory modules of potentially co-regulated genes. As the degree of similarity is expected to depend on the phylogenetic distance of homologs or orthologs, we favor an approach that is based on a comparison paradigm. The paper introduces a novel concept for measuring the similarity ofcis-regulatory modules which can then be used in an algorithm for comparing regulatory regions. The proposed algorithm searches for pairs of similar modules, and a prototype implementation is applied to human and mouse liver sequences. The results are compared to that of random sequences, and it is shown that a clear decision about co-regulation is possible at this level.
Authors:
K Ecker; L Welch
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Publication Detail:
Type:  Journal Article    
Journal Detail:
Title:  In silico biology     Volume:  9     ISSN:  1386-6338     ISO Abbreviation:  In Silico Biol. (Gedrukt)     Publication Date:  2009  
Date Detail:
Created Date:  2012-03-20     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9815902     Medline TA:  In Silico Biol     Country:  Netherlands    
Other Details:
Languages:  eng     Pagination:  285-306     Citation Subset:  IM    
Affiliation:
Russ College of Engineering and Technology, Ohio University, Athens, Ohio, USA.
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