MeSH-Informed Enrichment Analysis and MeSH-Guided Semantic Similarity Among Functional Terms and Gene Products in Chicken.
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 datasets that were employed represent (i) differentially expressed genes, and (ii) candidate genes under selective sweep or epistatic selection. The comparison of MeSH with GO overrepresentation analyses suggested not only that MeSH supports the findings obtained from GO analysis, but also that MeSH is able to further enrich the representation of biological knowledge and often provide more interpretable results. Based on the hierarchical structures of MeSH and GO, we computed semantic similarities among vocabularies, as well as semantic similarities among selected genes. These yielded the similarity levels between significant functional terms, and the annotation of each gene yielded the measures of gene similarity. Our findings show the benefits of using MeSH as an alternative choice of annotation in order to draw biological inferences from a list of genes of interest. We argue that the use of MeSH in conjunction with GO will be instrumental in facilitating the understanding of the genetic basis of complex traits.
Department of Animal Science, University of Nebraska-Lincoln, Nebraska 68583 morota@unl.edu.
Gota
G
Morota
United States Department of Agriculture, Agricultural Research Service, Columbia, Missouri Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211.
Timothy M
TM
Beissinger
Department of Animal Sciences, University of Florida, Gainesville, Florida University of Florida Genetics Institute, University of Florida, Gainesville, Florida 32610.
Francisco
0000-0001-6661-3991
F
Peñagaricano
D000818:Animals; D002645:Chickens / Q000145:classification / Q000235:genetics*; D030541:Databases, Genetic; D063990:Gene Ontology; D006801:Humans; D046650:Medical Subject Headings; D012660:Semantics; D009626:Terminology as Topic; D018875:Vocabulary, Controlled
MeSH; annotation; chicken; enrichment analysis; semantic similarity