Department of Medicine, Division of Infectious Diseases and Immunology
Animals; Databases, Genetic; *Gene Expression; Genomics; Humans; Mice; MicroRNAs; Oligonucleotide Array Sequence Analysis; RNA, Messenger
Immunology and Infectious Disease
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.
DOI of Published Version
BMC Bioinformatics. 2010 May 18;11:257. Link to article on publisher's site
Madden SF, Carpenter SB, Jeffery IB, Bjorkbacka H, Fitzgerald KA, O'Neill LA, Higgins DG. (2010). Detecting microRNA activity from gene expression data. Infectious Diseases and Immunology Publications. https://doi.org/10.1186/1471-2105-11-257. Retrieved from https://escholarship.umassmed.edu/infdis_pp/53