Nucleic Acids Research, 2001, Vol. 29, No. 1 246-254
© 2001 Oxford University Press
ARED: human AU-rich element-containing mRNA database reveals an unexpectedly diverse functional repertoire of encoded proteins
Department of Biostatistics, Epidemiology and Scientific Computing (Bioinformatics Section) and 1Department of Biological and Medical Research, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia and 2Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
The adenylate uridylate-rich elements (AREs) mediate the rapid turnover of mRNAs encoding proteins that regulate cellular growth and body response to exogenous agents such as microbes, inflammatory and environmental stimuli. However, the full repertoire of ARE-containing mRNAs is unknown. Here, we explore the distribution of AREs in human mRNA sequences. Computational derivation of a 13-bp ARE pattern was performed using multiple expectation maximization for motif elicitations (MEME) and consensus analyses. This pattern was statistically validated for the specificity towards the 3'-untranslated region and not coding region. The computationally derived ARE pattern is the basis of a database which contains non-redundant full-length ARE-mRNAs. The ARE-mRNA database (ARED; http://rc.kfshrc.edu.sa/ared) reveals that ARE-mRNAs encode a wide repertoire of functionally diverse proteins that belong to different biological processes and are important in several disease states. Cluster analysis was performed using the ARE sequences to demonstrate potential relationships between the type and number of ARE motifs, and the functional characteristics of the proteins.
* To whom correspondence should be addressed at: Head, Interferon and Cytokine Research Unit (MBC-03), Senior Scientist, Department of Biological and Medical Research, PO Box 3354, MBC-03, Riyadh 11211, Saudi Arabia. Tel: +966 1 442 7876; Fax: +966 1 442 7858; Email: khabar{at}kfshrc.edu.sa
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