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PMID: 20071740 Published · ppublish English Comparative Study Evaluation Study Journal Article Research Support, Non-U.S. Gov't

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

Nucleic acids research ·Vol. 38 ·No. 7 ·2010-04-00 ·Pages e97

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

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.

MeSH Terms
3' Untranslated Regions Alternative Splicing Computational Biology/methods Gene Expression Profiling/methods Humans MicroRNAs/chemistry,metabolism Oligonucleotide Array Sequence Analysis Oligonucleotide Probes RNA, Messenger/metabolism
Chemicals
3' Untranslated Regions MicroRNAs Oligonucleotide Probes RNA, Messenger
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Sales Gabriele
Department of Biology, University of Padova, 35121 Padova, Italy.
Coppe Alessandro
Bicciato Silvio
Bortoluzzi Stefania
Romualdi Chiara
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkp1239
Published
2010-04-00
Epub
2010-00-13
Pages
e97
Language
English
Region
England
NLM ID
0411011
PMCID
PMC2853140
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkp1239 PMC Full Text View journal details
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