Nucleic Acids Research

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
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Article

ARED 3.0: the large and diverse AU-rich transcriptome

Tala Bakheet, Bryan R. G. Williams² and Khalid S. A. Khabar^1,2,*

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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