Document Detail


Computational tools and resources for prediction and analysis of gene regulatory regions in the chick genome.
MedLine Citation:
PMID:  23355428     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
The discovery of cis-regulatory elements is a challenging problem in bioinformatics, owing to distal locations and context-specific roles of these elements in controlling gene regulation. Here we review the current bioinformatics methodologies and resources available for systematic discovery of cis-acting regulatory elements and conserved transcription factor binding sites in the chick genome. In addition, we propose and make available, a novel workflow using computational tools that integrate CTCF analysis to predict putative insulator elements, enhancer prediction, and TFBS analysis. To demonstrate the usefulness of this computational workflow, we then use it to analyze the locus of the gene Sox2 whose developmental expression is known to be controlled by a complex array of cis-acting regulatory elements. The workflow accurately predicts most of the experimentally verified elements along with some that have not yet been discovered. A web version of the CTCF tool, together with instructions for using the workflow can be accessed from http://toolshed.g2.bx.psu.edu/view/mkhan1980/ctcf_analysis. For local installation of the tool, relevant Perl scripts and instructions are provided in the directory named "code" in the supplementary materials.
Authors:
Mohsin A F Khan; Luz Mayela Soto-Jimenez; Timothy Howe; Andrea Streit; Alona Sosinsky; Claudio D Stern
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't; Review     Date:  2013-03-30
Journal Detail:
Title:  Genesis (New York, N.Y. : 2000)     Volume:  51     ISSN:  1526-968X     ISO Abbreviation:  Genesis     Publication Date:  2013 May 
Date Detail:
Created Date:  2013-05-24     Completed Date:  2013-12-31     Revised Date:  2014-02-20    
Medline Journal Info:
Nlm Unique ID:  100931242     Medline TA:  Genesis     Country:  United States    
Other Details:
Languages:  eng     Pagination:  311-24     Citation Subset:  IM    
Copyright Information:
Copyright © 2013 Wiley Periodicals, Inc.
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MeSH Terms
Descriptor/Qualifier:
Animals
Chickens / genetics*
Computational Biology / methods*
Databases, Nucleic Acid
Gene Expression Regulation*
Gene Regulatory Networks*
Genome*
Genomics / methods
Internet
Software
Workflow
Grant Support
ID/Acronym/Agency:
249892//European Research Council; BB/G000972/1//Biotechnology and Biological Sciences Research Council; G0400559//Medical Research Council; G0700095//Medical Research Council; //Biotechnology and Biological Sciences Research Council
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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