Detecting MicroRNA Signatures Using Gene Expression Analysis View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2014

AUTHORS

Stijn van Dongen , Anton J. Enright

ABSTRACT

Small RNAs such as microRNAs (miRNAs) have been shown to play important roles in genetic regulation of plants and animals. In particular, the miRNAs of animals are capable of downregulating large numbers of genes by binding to and repressing target genes. Although large numbers of miRNAs have been cloned and sequenced, methods for analyzing their targets are far from perfect. Methods exist that can predict the likely binding sites of miRNAs in target transcripts using sequence alignment, thermodynamics or machine learning approaches. It has been widely illustrated that such de novo computational approaches suffer from high false-positive and false-negative error rates. In particular these approaches do not take into account expression information regarding the miRNA or its target transcript. In this chapter we describe the use of miRNA seed enrichment analysis approaches to this problem. In cases where gene or protein expression data are available, it is possible to detect the signature of miRNA binding events by looking for enrichment of microRNA seed binding motifs in sorted gene lists. In this chapter we introduce the concept of miRNA target analysis, the background to motif enrichment analysis, and a number of programs designed for this purpose. We focus on the Sylamer algorithm for miRNA seed enrichment analysis and its applications for miRNA target discovery with examples from real biological datasets. More... »

PAGES

129-150

References to SciGraph publications

  • 2009-05. Mutations in the seed region of human miR-96 are responsible for nonsyndromic progressive hearing loss in NATURE GENETICS
  • 2009-05. An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice in NATURE GENETICS
  • 2005-02. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs in NATURE
  • 2001-02. Regulatory element detection using correlation with expression in NATURE GENETICS
  • 2003-12. MicroRNA targets in Drosophila in GENOME BIOLOGY
  • 2002-08. An algorithm for finding protein–DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments in NATURE BIOTECHNOLOGY
  • 2000-02. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans in NATURE
  • 2008-12. Detecting microRNA binding and siRNA off-target effects from expression data in NATURE METHODS
  • 2005-05. Combinatorial microRNA target predictions in NATURE GENETICS
  • 2010-12. Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis in BMC GENOMICS
  • 2008-09. Widespread changes in protein synthesis induced by microRNAs in NATURE
  • 2006-03. 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets in NATURE METHODS
  • 2008-10. Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences in NATURE PROTOCOLS
  • 2003-06. Expression profiling reveals off-target gene regulation by RNAi in NATURE BIOTECHNOLOGY
  • Book

    TITLE

    Springer Handbook of Bio-/Neuroinformatics

    ISBN

    978-3-642-30573-3
    978-3-642-30574-0

    Author Affiliations

    Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/978-3-642-30574-0_9

    DOI

    http://dx.doi.org/10.1007/978-3-642-30574-0_9

    DIMENSIONS

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