Computational challenges in miRNA target predictions: To be or not to be a true target?

Andrea Masotti, Christian Barbato, Ivan Arisi, Marcos E. Frizzo, Rossella Brandi, Letizia Da Sacco

Research output: Contribution to journalArticle

69 Citations (Scopus)

Abstract

All microRNA (miRNA) targetfinder algorithms return lists of candidate target genes. How valid is that output in a biological setting? Transcriptome analysis has proven to be a useful approach to determine mRNA targets. Time course mRNA microarray experiments may reliably identify downregulated genes in response to overexpression of specific miRNA. The approach may miss some miRNA targets that are principally downregulated at the protein level. However, the high-throughput capacity of the assay makes it an effective tool to rapidly identify a large number of promising miRNA targets. Finally, loss and gain of function miRNA genetics have the clear potential of being critical in evaluating the biological relevance of thousands of target genes predicted by bioinformatic studies and to test the degree to which miRNA-mediated regulation of any validated target functionally matters to the animal or plant.

Original languageEnglish
Article number803069
JournalJournal of Biomedicine and Biotechnology
Volume2009
DOIs
Publication statusPublished - 2009

Fingerprint

MicroRNAs
Down-Regulation
Genes
Messenger RNA
Gene Expression Profiling
Computational Biology
Proteins

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Medicine
  • Genetics
  • Molecular Biology
  • Health, Toxicology and Mutagenesis
  • Medicine(all)

Cite this

Computational challenges in miRNA target predictions : To be or not to be a true target? / Masotti, Andrea; Barbato, Christian; Arisi, Ivan; Frizzo, Marcos E.; Brandi, Rossella; Da Sacco, Letizia.

In: Journal of Biomedicine and Biotechnology, Vol. 2009, 803069, 2009.

Research output: Contribution to journalArticle

Masotti, Andrea ; Barbato, Christian ; Arisi, Ivan ; Frizzo, Marcos E. ; Brandi, Rossella ; Da Sacco, Letizia. / Computational challenges in miRNA target predictions : To be or not to be a true target?. In: Journal of Biomedicine and Biotechnology. 2009 ; Vol. 2009.
@article{32596500e17f40f4823645ffb9ff8041,
title = "Computational challenges in miRNA target predictions: To be or not to be a true target?",
abstract = "All microRNA (miRNA) targetfinder algorithms return lists of candidate target genes. How valid is that output in a biological setting? Transcriptome analysis has proven to be a useful approach to determine mRNA targets. Time course mRNA microarray experiments may reliably identify downregulated genes in response to overexpression of specific miRNA. The approach may miss some miRNA targets that are principally downregulated at the protein level. However, the high-throughput capacity of the assay makes it an effective tool to rapidly identify a large number of promising miRNA targets. Finally, loss and gain of function miRNA genetics have the clear potential of being critical in evaluating the biological relevance of thousands of target genes predicted by bioinformatic studies and to test the degree to which miRNA-mediated regulation of any validated target functionally matters to the animal or plant.",
author = "Andrea Masotti and Christian Barbato and Ivan Arisi and Frizzo, {Marcos E.} and Rossella Brandi and {Da Sacco}, Letizia",
year = "2009",
doi = "10.1155/2009/803069",
language = "English",
volume = "2009",
journal = "Journal of Biomedicine and Biotechnology",
issn = "1110-7243",
publisher = "Hindawi Publishing Corporation",

}

TY - JOUR

T1 - Computational challenges in miRNA target predictions

T2 - To be or not to be a true target?

AU - Masotti, Andrea

AU - Barbato, Christian

AU - Arisi, Ivan

AU - Frizzo, Marcos E.

AU - Brandi, Rossella

AU - Da Sacco, Letizia

PY - 2009

Y1 - 2009

N2 - All microRNA (miRNA) targetfinder algorithms return lists of candidate target genes. How valid is that output in a biological setting? Transcriptome analysis has proven to be a useful approach to determine mRNA targets. Time course mRNA microarray experiments may reliably identify downregulated genes in response to overexpression of specific miRNA. The approach may miss some miRNA targets that are principally downregulated at the protein level. However, the high-throughput capacity of the assay makes it an effective tool to rapidly identify a large number of promising miRNA targets. Finally, loss and gain of function miRNA genetics have the clear potential of being critical in evaluating the biological relevance of thousands of target genes predicted by bioinformatic studies and to test the degree to which miRNA-mediated regulation of any validated target functionally matters to the animal or plant.

AB - All microRNA (miRNA) targetfinder algorithms return lists of candidate target genes. How valid is that output in a biological setting? Transcriptome analysis has proven to be a useful approach to determine mRNA targets. Time course mRNA microarray experiments may reliably identify downregulated genes in response to overexpression of specific miRNA. The approach may miss some miRNA targets that are principally downregulated at the protein level. However, the high-throughput capacity of the assay makes it an effective tool to rapidly identify a large number of promising miRNA targets. Finally, loss and gain of function miRNA genetics have the clear potential of being critical in evaluating the biological relevance of thousands of target genes predicted by bioinformatic studies and to test the degree to which miRNA-mediated regulation of any validated target functionally matters to the animal or plant.

UR - http://www.scopus.com/inward/record.url?scp=68149171901&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=68149171901&partnerID=8YFLogxK

U2 - 10.1155/2009/803069

DO - 10.1155/2009/803069

M3 - Article

C2 - 19551154

AN - SCOPUS:68149171901

VL - 2009

JO - Journal of Biomedicine and Biotechnology

JF - Journal of Biomedicine and Biotechnology

SN - 1110-7243

M1 - 803069

ER -