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Related Concept Videos

MicroRNAs01:22

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...
MicroRNAs01:22

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...
MicroRNAs01:22

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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...
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Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Cerebrospinal Fluid MicroRNA Profiling Using Quantitative Real Time PCR
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Correlation of expression profiles between microRNAs and mRNA targets using NCI-60 data.

Yu-Ping Wang1, Kuo-Bin Li

  • 1Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan.

BMC Genomics
|May 14, 2009
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This study shows that correlating microRNA (miRNA) and mRNA expression profiles can help identify functional miRNA-mRNA relationships. Negative correlations were more common for predicted targets, suggesting expression data aids in computational target identification.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression.
  • miRNA function is often assessed by their ability to down-regulate target mRNAs.
  • Analyzing expression data can help identify functional miRNA-mRNA interactions.

Purpose of the Study:

  • To investigate if correlations in miRNA and mRNA expression profiles can identify functional miRNA-mRNA relationships.
  • To compare miRNA-mRNA correlations between different prediction databases (TargetScan, miRBase).
  • To explore correlations for experimentally validated miRNA targets and intronic miRNAs.

Main Methods:

  • Computed Pearson correlation coefficients between miRNA and mRNA expression profiles using NCI-60 data.
  • Utilized predicted miRNA-mRNA interactions from TargetScan 4.1 and miRBase release 5.
  • Applied Benjamini and Hochberg correction to correlation coefficients.

Main Results:

  • TargetScan-predicted interactions showed a higher percentage of negative expression correlations than miRBase-predicted pairs.
  • Genes in mRNA degradation pathways exhibited more negative miRNA-mRNA correlations than those in translational repression.
  • Intronic miRNAs and their host genes displayed positive expression profile correlations.

Conclusions:

  • Expression profile correlations can computationally assist in identifying functional miRNA-target associations.
  • Negatively correlated expression profiles are more likely for TargetScan-predicted interactions.
  • Expression profiles serve as a supplementary tool for miRNA-mRNA interaction discovery.