ARED 3.0: the large and diverse AU-rich transcriptome

By Tala Bakheet, Bryan R. G. Williams, Khalid S. A. Khabar. Nucleic Acids Res., 2005

340 citations recorded by the source corpus.

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 . 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.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/6b14f8d0a2c61485988cc007e73fdd33e3ba4b53

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Citations in the corpus

MiR-15a and miR-16-1 cluster functions in human leukemia (2008, methodology): “sa/ared/), as described (44), was used (for details see SI Text).”
Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development (2009, background): “For example, in humans, the AU-rich elements (AREs) involved in control of mRNA stability are found in 5–8% of all genes (6), and over 30% of genes are predicted to have miRNA target sites (7).”
Regulation of cytoplasmic mRNA decay (2012, neutral): “If they are classified by sequence alone, canonical ARE-containing mRNAs constitute up to 9% of cellular mRNA”