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

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

doi:10.1186/s12859-015-0453-z

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

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

Animal Science

Research output: Contribution to journal › Article › peer-review

21 Scopus citations

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 language	English (US)
Article number	45
Journal	BMC bioinformatics
Volume	16
Issue number	1
DOIs	https://doi.org/10.1186/s12859-015-0453-z
State	Published - Feb 6 2015

Keywords

Annotation
Enrichment analysis
MeSH
Over-representation analysis

ASJC Scopus subject areas

Structural Biology
Biochemistry
Molecular Biology
Computer Science Applications
Applied Mathematics

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10.1186/s12859-015-0453-z

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title = "MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis",

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.",

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AU - Ishii, Manabu

AU - Nakazato, Takeru

AU - Miyazaki, Satoru

AU - Nikaido, Itoshi

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