Using expression profiling data to identify human microRNA targets

Jim C. Huang, Tomas Babak, Timothy Corson, Gordon Chua, Sofia Khan, Brenda L. Gallie, Timothy R. Hughes, Benjamin J. Blencowe, Brendan J. Frey, Quaid D. Morris

Research output: Contribution to journalArticle

322 Citations (Scopus)

Abstract

We demonstrate that paired expression profiles of microRNAs (miRNAs) and mRNAs can be used to identify functional miRNA-target relationships with high precision. We used a Bayesian data analysis algorithm, GenMiR++, to identify a network of 1,597 high-confidence target predictions for 104 human miRNAs, which was supported by RNA expression data across 88 tissues and cell types, sequence complementarity and comparative genomics data. We experimentally verified our predictions by investigating the result of let-7b downregulation in retinoblastoma using quantitative reverse transcriptase (RT)-PCR and microarray profiling: some of our verified let-7b targets include CDC25A and BCL7A. Compared to sequence-based predictions, our high-scoring GenMiR++ predictions had much more consistent Gene Ontology annotations and were more accurate predictors of which mRNA levels respond to changes in let-7b levels.

Original languageEnglish (US)
Pages (from-to)1045-1049
Number of pages5
JournalNature Methods
Volume4
Issue number12
DOIs
StatePublished - Dec 2007
Externally publishedYes

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MicroRNAs
Molecular Sequence Annotation
Messenger RNA
Gene Ontology
Bayes Theorem
Retinoblastoma
Genomics
Reverse Transcriptase Polymerase Chain Reaction
RNA-Directed DNA Polymerase
Down-Regulation
Microarrays
RNA
Ontology
Genes
Tissue

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Cell Biology

Cite this

Huang, J. C., Babak, T., Corson, T., Chua, G., Khan, S., Gallie, B. L., ... Morris, Q. D. (2007). Using expression profiling data to identify human microRNA targets. Nature Methods, 4(12), 1045-1049. https://doi.org/10.1038/nmeth1130

Using expression profiling data to identify human microRNA targets. / Huang, Jim C.; Babak, Tomas; Corson, Timothy; Chua, Gordon; Khan, Sofia; Gallie, Brenda L.; Hughes, Timothy R.; Blencowe, Benjamin J.; Frey, Brendan J.; Morris, Quaid D.

In: Nature Methods, Vol. 4, No. 12, 12.2007, p. 1045-1049.

Research output: Contribution to journalArticle

Huang, JC, Babak, T, Corson, T, Chua, G, Khan, S, Gallie, BL, Hughes, TR, Blencowe, BJ, Frey, BJ & Morris, QD 2007, 'Using expression profiling data to identify human microRNA targets', Nature Methods, vol. 4, no. 12, pp. 1045-1049. https://doi.org/10.1038/nmeth1130
Huang JC, Babak T, Corson T, Chua G, Khan S, Gallie BL et al. Using expression profiling data to identify human microRNA targets. Nature Methods. 2007 Dec;4(12):1045-1049. https://doi.org/10.1038/nmeth1130
Huang, Jim C. ; Babak, Tomas ; Corson, Timothy ; Chua, Gordon ; Khan, Sofia ; Gallie, Brenda L. ; Hughes, Timothy R. ; Blencowe, Benjamin J. ; Frey, Brendan J. ; Morris, Quaid D. / Using expression profiling data to identify human microRNA targets. In: Nature Methods. 2007 ; Vol. 4, No. 12. pp. 1045-1049.
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