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 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.
authors.affiliation: 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.|Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Saitama, Japan. j3b12703@ed.tus.ac.jp.
authors.forename: Koki
authors.initials: K
authors.lastname: Tsuyuzaki
authors.affiliation: Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA. morota@ansci.wisc.edu.|Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, USA. morota@ansci.wisc.edu.
authors.forename: Gota
authors.initials: G
authors.lastname: Morota
authors.affiliation: Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Saitama, Japan. manabu.ishii@riken.jp.
authors.forename: Manabu
authors.initials: M
authors.lastname: Ishii
authors.affiliation: 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.
authors.forename: Takeru
authors.initials: T
authors.lastname: Nakazato
authors.affiliation: 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.
authors.forename: Satoru
authors.initials: S
authors.lastname: Miyazaki
authors.affiliation: Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Saitama, Japan. itoshi.nikaido@riken.jp.
authors.forename: Itoshi
authors.initials: I
authors.lastname: Nikaido
mesh_terms: D000818:Animals; D031204:Caloric Restriction; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling; D055106:Genome-Wide Association Study; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D046650:Medical Subject Headings; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis; D011550:Pseudomonas aeruginosa / Q000235:genetics; D039781:PubMed; D051381:Rats; D012984:Software; D018875:Vocabulary, Controlled