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Nucleic Acids Research 2006 34(Database Issue):D111-D114; doi:10.1093/nar/gkj052
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Nucleic Acids Research, 2006, Vol. 34, Database issue D111-D114
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

ARED 3.0: the large and diverse AU-rich transcriptome

Tala Bakheet, Bryan R. G. Williams2 and Khalid S. A. Khabar1,2,*

Department of Biostatistics, Epidemiology, and Scientific Computing (Bioinformatics Section), King Faisal Specialist Hospital and Research Center Riyadh 11211, Saudi Arabia 1Department of Biological and Medical Research, King Faisal Specialist Hospital and Research Center Riyadh 11211, Saudi Arabia 2Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Foundation Cleveland, OH 44195, USA

*To whom correspondence should be addressed. Tel: +1 966 1 442 7876, Fax: +1 966 1 442 7858; Email: khabar{at}kfshrc.edu.sa

Received August 16, 2005. Revised October 4, 2005. Accepted October 4, 2005.

A comprehensive search that utilized a large set of mRNA data from human genome databases and additionally, expressed sequence tag (EST) database characterized this latest update of AU-rich elements (AREs) containing mRNA database (ARED). A large number of ARE-mRNA, as much as 4000, were recovered and include many of ARE alternative forms. This number represents as much as 5–8% of the human genes depending on the entire number of genes. The new ARED does not contain only larger and diverse number of ARE-mRNAs but additional functionality and enhanced search capabilities are given in the database website http://rc.kfshrc.edu.sa/ared/. These include class and cluster of AREs, source mRNAs, EST evidence, buildup information, retrieval of lists of genes, and integration with current and new NCBI data, such as Entrez ID and Unigene. Gene Ontology analysis shows there are significant differences in functional diversity of ARED when compared with the overall genome. Many of ARE-genes mediate regulatory processes, reactions to outside stimuli, RNA metabolism, and developmental processes particularly those of early and transient responses. The wide interest in mRNA turnover and importance of AREs in health and disease signify the compilation of ARE-genes.


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