Detecting microRNA activity from gene expression data.
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.
Madden
Stephen F
SF
School of Medicine and Medical Science, Conway Institute, University College Dublin, Dublin, Ireland.
Carpenter
Susan B
SB
Jeffery
Ian B
IB
Björkbacka
Harry
H
Fitzgerald
Katherine A
KA
O'Neill
Luke A
LA
Higgins
Desmond G
DG
D000818:Animals; D030541:Databases, Genetic; D015870:Gene Expression; D023281:Genomics / Q000379:methods*; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism
D035683:MicroRNAs; D012333:RNA, Messenger