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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...
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mirPub: a database for searching microRNA publications.

Thanasis Vergoulis1, Ilias Kanellos1, Nikos Kostoulas2

  • 1School of Electrical and Computer Engineering, NTUA, Zografou 15773, IMIS Institute, 'Athena' RC, Marousi 15125, DIANA-Lab, Institute of Molecular Oncology, BSRC 'Alexander Fleming', Vari 16672, Department of Computer & Communication Engineering, University of Thessaly, Volos 38221, Greece and School of Computer Science & Info Tech, RMIT University, Melbourne 3001, Australia School of Electrical and Computer Engineering, NTUA, Zografou 15773, IMIS Institute, 'Athena' RC, Marousi 15125, DIANA-Lab, Institute of Molecular Oncology, BSRC 'Alexander Fleming', Vari 16672, Department of Computer & Communication Engineering, University of Thessaly, Volos 38221, Greece and School of Computer Science & Info Tech, RMIT University, Melbourne 3001, Australia.

Bioinformatics (Oxford, England)
|December 21, 2014
PubMed
Summary

Searching for microRNA (miRNA) literature is challenging due to inconsistent naming. The mirPub database offers an intuitive solution for effective miRNA research by integrating text mining and crowdsourcing.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Keyword searches in MEDLINE for microRNA (miRNA) literature face significant obstacles.
  • miRNA nomenclature inconsistencies and evolution complicate literature retrieval.
  • Standard nomenclature issues can lead to misidentification of miRNA molecules.

Purpose of the Study:

  • To develop a robust database and interface for searching miRNA-related publications.
  • To address the challenges posed by non-standard miRNA naming conventions.
  • To facilitate efficient and accurate retrieval of relevant miRNA literature.

Main Methods:

  • Utilized text mining techniques on MEDLINE data.
  • Integrated information from multiple curated databases.
  • Incorporated a crowdsourcing approach for user community data.
  • Developed an intuitive interface with interactive visualization tools.

Main Results:

  • mirPub provides a powerful and intuitive interface for miRNA literature searches.
  • The database addresses nomenclature issues through text mining and data integration.
  • Includes features like interactive visualizations, disease/cell type tag clouds, and TarBase integration.

Conclusions:

  • mirPub effectively overcomes obstacles in searching miRNA literature.
  • The database enhances the discoverability of relevant miRNA publications.
  • Offers advanced features for exploring miRNA data evolution and related genes.