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MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis.

Koki Tsuyuzaki1,2, Gota Morota3,4, Manabu Ishii5

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We developed a new framework for Medical Subject Headings (MeSH) over-representation analysis (ORA), simplifying gene list interpretation. This tool enhances biological insights by enabling easy retrieval of relevant PubMed documents based on enriched MeSH terms.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Over-representation analysis (ORA) is crucial for interpreting gene lists in genome-wide studies.
  • Medical Subject Headings (MeSH) offer broader biological context for ORA but existing tools are insufficient.

Purpose of the Study:

  • To develop an improved framework for MeSH-based ORA.
  • To provide a user-friendly platform for enhanced biological interpretation of gene sets.

Main Methods:

  • Developed a novel MeSH ORA framework utilizing six R packages: MeSH.db, MeSH.AOR.db, MeSH.PCR.db, org.MeSH.XXX.db, MeSHDbi, and meshr.

Main Results:

  • The framework facilitates straightforward MeSH ORA execution.
  • Enriched MeSH terms can be used to retrieve and save relevant PubMed documents locally.

Conclusions:

  • The developed framework simplifies MeSH ORA, improving biological interpretation.
  • Users can efficiently access and manage PubMed literature associated with enriched MeSH terms.