Impact of probe annotation on the integration of miRNA-mRNA expression profiles for miRNA target detection.

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 Res

journal_title

Nucleic acids research

authors

Sales G,Coppe A,Bicciato S,Bortoluzzi S,Romualdi C

doi

10.1093/nar/gkp1239

subject

Has Abstract

pub_date

2010-04-01 00:00:00

pages

e97

issue

7

eissn

0305-1048

issn

1362-4962

pii

gkp1239

journal_volume

38

pub_type

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