ArticleBMC bioinformatics2015
MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
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- pyMeSHSim: an integrative python package for biomedical named entity recognition, normalization, and comparison of MeSH terms.BMC bioinformatics · 2020Article
- Fine mapping of genomic regions associated with female fertility in Nellore beef cattle based on sequence variants from segregating sires.Journal of animal science and biotechnology · 2019Article
- Integrating bioinformatics approaches for a comprehensive interpretation of metabolomics datasets.Current opinion in biotechnology · 2018Review
- Genetic dissection of bull fertility in US Jersey dairy cattle.Animal genetics · 2018Article
- RNA-Seq reveals novel genes and pathways involved in bovine mammary involution during the dry period and under environmental heat stress.Scientific reports · 2018Article
- RNA-Seq Analysis of IL-1B and IL-36 Responses in Epidermal Keratinocytes Identifies a Shared MyD88-Dependent Gene Signature.Frontiers in immunology · 2018Article
- GM604 regulates developmental neurogenesis pathways and the expression of genes associated with amyotrophic lateral sclerosis.Translational neurodegeneration · 2018Article
- Using scale and feather traits for module construction provides a functional approach to chicken epidermal development.Functional & integrative genomics · 2017Article
- Genomic study and Medical Subject Headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers.Journal of animal science · 2017Article
- Medical Subject Heading (MeSH) annotations illuminate maize genetics and evolution.Plant methods · 2017Article
- Unravelling the genomic architecture of bull fertility in Holstein cattle.BMC genetics · 2016Article
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6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundIn 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.
resultsIn 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.
conclusionsUsing 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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