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

Koki Tsuyuzaki, Gota Morota, Manabu Ishii, Takeru Nakazato, Satoru Miyazaki, Itoshi Nikaido

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Background: In genome-wide studies, over-representation analysis (ORA) against a set of genes is an essential step for biological interpretation. Many gene annotation resources and software platforms for ORA have been proposed. Recently, Medical Subject Headings (MeSH) terms, which are annotations of PubMed documents, have been used for ORA. MeSH enables the extraction of broader meaning from the gene lists and is expected to become an exhaustive annotation resource for ORA. However, the existing MeSH ORA software platforms are still not sufficient for several reasons. Results: In this work, we developed an original MeSH ORA framework composed of six types of R packages, including, the -type packages, and. Conclusions: Using our framework, users can easily conduct MeSH ORA. By utilizing the enriched MeSH terms, related PubMed documents can be retrieved and saved on local machines within this framework.

Original languageEnglish (US)
Article number45
JournalBMC bioinformatics
Volume16
Issue number1
DOIs
StatePublished - Feb 6 2015

Fingerprint

Medical Subject Headings
Genes
Annotation
PubMed
Gene
Software
Molecular Sequence Annotation
Essential Genes
Resources
Term
Framework
Genome
Sufficient

Keywords

  • Annotation
  • Enrichment analysis
  • MeSH
  • Over-representation analysis

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

MeSH ORA framework : R/Bioconductor packages to support MeSH over-representation analysis. / Tsuyuzaki, Koki; Morota, Gota; Ishii, Manabu; Nakazato, Takeru; Miyazaki, Satoru; Nikaido, Itoshi.

In: BMC bioinformatics, Vol. 16, No. 1, 45, 06.02.2015.

Research output: Contribution to journalArticle

Tsuyuzaki, Koki ; Morota, Gota ; Ishii, Manabu ; Nakazato, Takeru ; Miyazaki, Satoru ; Nikaido, Itoshi. / MeSH ORA framework : R/Bioconductor packages to support MeSH over-representation analysis. In: BMC bioinformatics. 2015 ; Vol. 16, No. 1.
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