MeSH Annotation of the Chicken Genome

Biomedical vocabularies and ontologies aid in recapitulating biological knowledge. Annotation of gene products is mainly accelerated by Gene Ontology (GO) and more recently by Medical Subject Headings (MeSH). MeSH is the National Library of Medicine's controlled vocabulary and it is making inroads into annotation enrichment analysis. The availability of MeSH annotation in farm animals poses both new challenges and opportunities for downstream analysis in functional genomic studies. Here we investigated well-curated MeSH and GO terms to characterize the lists of selected chicken genes available at public repositories: differentially expressed genes from RNA-seq and genes subjected to sweeps and/or epistatic selection. The comparison of MeSH with GO overrepresentation analyses suggested not only that MeSH supports findings obtained from GO but also that MeSH is able to further enrich the representation of biological knowledge. Based on the hierarchical structures of MeSH and GO, respectively, we computed the semantic similarity between vocabularies as well as the similarity between selected genes. The respective hierarchies of MeSH and GO yielded the similarity levels between significant terms and the annotation of each yielded the measures of gene similarity. Special attention is paid to a pair of genes showing high similarity in both MeSH and GO-based measures or in only one of them. We argue that the use of MeSH in conjunction with GO will be instrumental in facilitating the biological interpretation when a set of selected genes is identified.