Nucleic Acids Research

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Nucleic Acids Research, 2003, Vol. 31, No. 1 421-423
© 2003 Oxford University Press

ARED 2.0: an update of AU-rich element mRNA database

Tala Bakheet¹, Bryan R. G. Williams³ and Khalid S. A. Khabar^*,2,3

¹ Department of Biostatistics, Epidemiology, and Scientific Computing (Bioinformatics Section), Riyadh 11211, Saudi Arabia ² Department of Biological and Medical Research, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia ³ Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA

*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 14427876; Fax: +966 14427858; Email: khabar{at}kfshrc.edu.sa

ABSTRACT

The Adenylate Uridylate (AU)-Rich Element Database, ARED-mRNA version 2.0, contains information not present in the previous ARED. This includes additional data entries, new information and links to Unigene, LocusLink, RefSeq records and mouse homologue data. An ARE consensus sequence specific to the 3'UTR is the basis of ARED that demonstrated two important findings: (i) AREs are present in a large, previously unrecognized set of human mRNAs; and (ii) ARE-mRNAs encode proteins of diverse functions which are largely involved in early and transient biological responses. In this update, we have modified the strategy for identifying ARE-mRNA in order to systematically deal with inconsistencies of molecule type and mRNA region in GenBank records. Potential uses for the ARED in functional genomics are also given. The database is accessible via the web, http://rc.kfshrc.edu.sa/ared, with a new querying system that allows searching ARE-mRNAs by any public database identifier or name. The ARED website also contains relevant links to uses for the ARED.

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