Abstract:
:MicroRNAs (miRNAs) are small non-coding RNAs that mediate gene expression at the post-transcriptional and translational levels by an imperfect binding to target mRNA 3'UTR regions. While the ab-initio computational prediction of miRNA-mRNA interactions still poses significant challenges, it is possible to overcome some of its limitations by carefully integrating into the analysis the paired expression profiles of miRNAs and mRNAs. In this work, we show how the choice of a proper probe annotation for microarray platforms is an essential requirement to achieve good sensitivity in the identification of miRNA-mRNA interactions. We compare the results obtained from the analysis of the same expression profiles using both gene and transcript based custom CDFs that we have developed for a number of different annotations (ENSEMBL, RefSeq, AceView). In all cases, transcript-based annotations clearly improve the effectiveness of data integration and thus provide a more reliable confirmation of computationally predicted miRNA-mRNA interactions.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Sales G,Coppe A,Bicciato S,Bortoluzzi S,Romualdi Cdoi
10.1093/nar/gkp1239subject
Has Abstractpub_date
2010-04-01 00:00:00pages
e97issue
7eissn
0305-1048issn
1362-4962pii
gkp1239journal_volume
38pub_type
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