Discovery and visualization of miRNA-mRNA functional modules within integrated data using bicluster analysis

Nucleic Acids Research
K BryanR L Stallings

Abstract

MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression at a post-transcriptional level. An miRNA may target many messenger RNA (mRNA) transcripts, and each transcript may be targeted by multiple miRNAs. Our understanding of miRNA regulation is evolving to consider modules of miRNAs that regulate groups of functionally related mRNAs. Here we expand the model of miRNA functional modules and use it to guide the integration of miRNA and mRNA expression and target prediction data. We present evidence of cooperativity between miRNA classes within this integrated miRNA-mRNA association matrix. We then apply bicluster analysis to uncover miRNA functional modules within this integrated data set and develop a novel application to visualize and query these results. We show that this wholly unsupervised approach can discover a network of miRNA-mRNA modules that are enriched for both biological processes and miRNA classes. We apply this method to investigate the interplay of miRNAs and mRNAs in integrated data sets derived from neuroblastoma and human immune cells. This study is the first to apply the technique of biclustering to model functional modules within an integrated miRNA-mRNA association matrix. Result...Continue Reading

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Citations

Nov 7, 2014·Interdisciplinary Sciences, Computational Life Sciences·Suza Mohammad NurTahmina Sharmin
Aug 1, 2015·Interdisciplinary Sciences, Computational Life Sciences·Suza Mohammad NurTahmina Sharmin
Dec 19, 2014·Interdisciplinary Sciences, Computational Life Sciences·Suza Mohammad NurTahmina Sharmin
Oct 8, 2016·BMC Genomics·Christian WakeRichard H Myers
Dec 21, 2014·Bioinformatics·Jun DingHaiyan Hu
Sep 22, 2019·Cells·Arthur C OliveiraDanillo Pinhal
Jun 24, 2019·Pathology, Research and Practice·Xi ChenYinghua Li

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Methods Mentioned

BETA
transfection
GTPase

Software Mentioned

mRNA Module Visualization Software
miRMAP
MirConnX
miRNA
BUBBLE
TargetScan
GenMiR
miR Module Analysis Program ( miRMAP )

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