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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

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...
Small interfering RNAs (siRNA)02:30

Small interfering RNAs (siRNA)

Small interfering RNAs, or siRNAs, are short regulatory RNA molecules that can silence genes post-transcriptionally, as well as the transcriptional level in some cases. siRNAs are important for protecting cells against viral infections and silencing transposable genetic elements.
In the cytoplasm, siRNA is processed from a double-stranded RNA, which comes from either endogenous DNA transcription or exogenous sources like a virus. This double-stranded RNA is then cleaved by the ATP-dependent...

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ComiR: Combinatorial microRNA target prediction tool.

Claudia Coronnello1, Panayiotis V Benos

  • 1Fondazione Ri.MED, 90133 Palermo, Italy. corocla@gmail.com

Nucleic Acids Research
|May 25, 2013
PubMed
Summary
This summary is machine-generated.

ComiR predicts microRNA (miRNA) gene targets by analyzing messenger RNA (mRNA) sequences and miRNA expression levels. This tool enhances regulatory potential predictions using thermodynamic modeling and machine learning for accurate target identification.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • MicroRNAs (miRNAs) are key regulators of gene expression.
  • Predicting miRNA targets is crucial for understanding gene regulation.
  • Existing methods may not fully capture combinatorial miRNA effects.

Purpose of the Study:

  • To develop a computational tool for predicting combinatorial miRNA targets on messenger RNAs (mRNAs).
  • To integrate miRNA expression levels with thermodynamic modeling and machine learning for enhanced prediction accuracy.
  • To provide a user-friendly platform for analyzing miRNA-mRNA interactions across multiple species.

Main Methods:

  • Development of the ComiR web tool.
  • Utilizing thermodynamic modeling and machine learning algorithms.
  • Incorporating user-provided miRNA expression data for combinatorial analysis.
  • Application to human, mouse, fly, and worm genomes.

Main Results:

  • ComiR computes the probability of an mRNA being a functional target of a set of miRNAs.
  • Predictions are based on relative miRNA expression levels and predicted binding sites.
  • The tool offers a user-friendly interface for data input and filtering.
  • Results are downloadable and visualizable for further analysis.

Conclusions:

  • ComiR provides an accurate and efficient method for combinatorial miRNA target prediction.
  • The tool facilitates the identification of relevant miRNA-mRNA interactions.
  • ComiR is a valuable resource for researchers in gene regulation and bioinformatics.