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BMC Bioinformatics. 2015 Feb 15;16:45. doi: 10.1186/s12859-015-0453-z.

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

Author information

1
Department of Medical and Life Science, Faculty of Pharmaceutical Science, Tokyo University of Science, 2641 Yamazaki, Noda, 278-8510, Chiba, Japan. j3b12703@ed.tus.ac.jp.
2
Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Saitama, Japan. j3b12703@ed.tus.ac.jp.
3
Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA. morota@ansci.wisc.edu.
4
Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, USA. morota@ansci.wisc.edu.
5
Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Saitama, Japan. manabu.ishii@riken.jp.
6
Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), Faculty of Engineering Building 12, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, 113-0032, Tokyo, Japan. nakazato@dbcls.rois.ac.jp.
7
Department of Medical and Life Science, Faculty of Pharmaceutical Science, Tokyo University of Science, 2641 Yamazaki, Noda, 278-8510, Chiba, Japan. smiyazak@rs.noda.tus.ac.jp.
8
Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Saitama, Japan. itoshi.nikaido@riken.jp.

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.

PMID:
25887539
PMCID:
PMC4343279
DOI:
10.1186/s12859-015-0453-z
[Indexed for MEDLINE]
Free PMC Article

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