Life Sciences Commons^™

Mesh-Informed Enrichment Analysis And Mesh-Guided Semantic Similarity Among Functional Terms And Gene Products In Chicken, Gota Morota, Timothy M. Beissinger, Francisco Peñagaricano

Department of Animal Science: Faculty Publications

Biomedical vocabularies and ontologies aid in recapitulating biological knowledge. The annotation of gene products is mainly accelerated by Gene Ontology (GO) and more recently by Medical Subject Headings (MeSH). Here we report a suite of MeSH packages for chicken in Bioconductor and illustrate some features of different MeSH-based analyses, including MeSH-informed enrichment analysis and MeSH-guided semantic similarity among terms and gene products, using two lists of chicken genes available in public repositories. The two published data sets that were employed represent (i) differentially expressed genes and (ii) candidate genes under selective sweep or epistatic selection. The comparison of MeSH with …

Mesh Ora Framework: R/Bioconductor Packages To Support Mesh Over-Representation Analysis, Koki Tsuyuzaki, Gota Morota, Manabu Ishii, Takeru Nakazato, Satoru Miyazaki, Itoshi Nikaido

Department of Animal Science: Faculty Publications

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 …

An Application Of Mesh Enrichment Analysis In Livestock, Gota Morota, F. Moreno, James L. Petersen, Daniel C. Ciobanu, K. Tsuyuzaki, I. Nikaido

Department of Animal Science: Faculty Publications

An integral part of functional genomics studies is to assess the enrichment of specific biological terms in lists of genes found to be playing an important role in biological phenomena. Contrasting the observed frequency of annotated terms with those of the background is at the core of overrepresentation analysis (ORA). Gene Ontology (GO) is a means to consistently classify and annotate gene products and has become a mainstay in ORA. Alternatively, Medical Subject Headings (MeSH) offers a comprehensive life science vocabulary including additional categories that are not covered by GO. Although MeSH is applied predominantly in human and model organism …