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

Authors

Koki Tsuyuzaki, Tokyo University of ScienceFollow
Gota Morota, University of Nebraska-LincolnFollow
Manabu Ishii, Center for Computing and Communication
Takeru Nakazato, University of Tokyo
Satoru Miyazaki, Tokyo University of Science
Itoshi Nikaido, Center for Computing and CommunicationFollow

Document Type

Article

Date of this Version

2015

Citation

Tsuyuzaki et al. BMC Bioinformatics (2015) 16:45. DOI 10.1186/s12859-015-0453-z

Comments

© 2015 Tsuyuzaki et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License. Used by permission.

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 MeSH.db, MeSH.AOR.db, MeSH.PCR.db, the org.MeSH.XXX.db-type packages, MeSHDbi, and meshr.

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.