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Please use this identifier to cite or link to this item: http://hdl.handle.net/2262/40099

Title: Detecting microRNA activity from gene expression data.
Author: O'NEILL, LUKE ANTHONY JOHN
CARPENTER, SUSAN
Sponsor: Science Foundation Ireland
Author's Homepage: http://people.tcd.ie/laoneill
Keywords: Biochemistry
MicroRNAs
Issue Date: 2010
Publisher: BioMed Central
Citation: Madden SF, Carpenter SB, Jeffery IB, Bjorkbacka H, Fitzgerald KA, O'Neill LA, Higgins DG, Detecting microRNA activity from gene expression data., BMC Bioinformatics, 11, 1, 2010, 257
Series/Report no.: BMC Bioinformatics;
11;
1;
Abstract: ABSTRACT: BACKGROUND: MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression by binding to the messenger RNA (mRNA) of protein coding genes. They control gene expression by either inhibiting translation or inducing mRNA degradation. A number of computational techniques have been developed to identify the targets of miRNAs. In this study we used predicted miRNA-gene interactions to analyse mRNA gene expression microarray data to predict miRNAs associated with particular diseases or conditions. RESULTS: Here we combine correspondence analysis, between group analysis and co-inertia analysis (CIA) to determine which miRNAs are associated with differences in gene expression levels in microarray data sets. Using a database of miRNA target predictions from TargetScan, TargetScanS, PicTar4way PicTar5way, and miRanda and combining these data with gene expression levels from sets of microarrays, this method produces a ranked list of miRNAs associated with a specified split in samples. We applied this to three different microarray datasets, a papillary thyroid carcinoma dataset, an in-house dataset of lipopolysaccharide treated mouse macrophages, and a multi-tissue dataset. In each case we were able to identified miRNAs of biological importance. CONCLUSIONS: We describe a technique to integrate gene expression data and miRNA target predictions from multiple sources.
Description: PUBLISHED
URI: http://hdl.handle.net/2262/40099
Related links: http://www.biomedcentral.com/1471-2105/11/257
Appears in Collections:Biochemistry (Scholarly Publications)

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