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A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
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Published on: August 21, 2019

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miRBase: from microRNA sequences to function

Ana Kozomara1, Maria Birgaoanu1, Sam Griffiths-Jones1

  • 1School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.

Nucleic Acids Research
|November 14, 2018
PubMed

Insights

The miRBase database (v22) now includes enhanced quality annotations and functional information for microRNA sequences across 271 organisms. This release improves microRNA research by validating gene annotations and summarizing cellular functions.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • miRBase is a comprehensive microRNA (miRNA) sequence database.
  • The latest release, v22, contains sequences from 271 organisms, including hairpin precursors and mature miRNAs.
  • Accurate miRNA annotations and functional information are crucial for biological research.

Purpose of the Study:

  • To describe improvements in the miRBase database and website.
  • To provide enhanced information on the quality of miRNA gene annotations.
  • To increase the availability of data on the cellular functions of miRNA products.

Main Methods:

  • Collected and mapped 5.5 billion small RNA deep sequencing reads to miRNA sequences.
  • Utilized read mapping patterns to assess the validity of miRNA annotations.
  • Implemented text-mining approaches on open-access articles to extract miRNA functional information.
  • Disseminated Gene Ontology (GO) terms annotated against miRBase sequences.

Main Results:

  • Read mapping provided strong support for 20-65% of miRNA annotations in animal genomes.
  • Evidence was found for the removal of over 200 sequences from the database.
  • Functional information was extracted from over 500,000 sentences across 18,542 papers, linked to 12,519 miRNA entries.
  • Text-mining generated sentence summaries and word clouds for miRNA functional information.

Conclusions:

  • miRBase v22 offers improved data quality and accessibility for miRNA research.
  • Enhanced annotations and functional information facilitate a deeper understanding of miRNA roles.
  • The database and its associated tools are publicly available to the scientific community.

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