ArticleNucleic acids research2010
Impact of probe annotation on the integration of miRNA-mRNA expression profiles for miRNA target detection.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- MiR-223-3p Regulates Autophagy and Inflammation by Targeting ATG16L1 in Fusarium solani-Induced Keratitis.Investigative ophthalmology & visual science · 2022Article
- Comprehensive annotation of microRNA expression profiles.BMC genetics · 2013Article
- Prioritizing cancer-related key miRNA-target interactions by integrative genomics.Nucleic acids research · 2012Article
- Up-regulation of microRNAs in brain of human alcoholics.Alcoholism, clinical and experimental research · 2011Article
- Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies.BMC bioinformatics · 2011Article
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Authors and funding
5 authors.
Funding
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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.
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