meshr

meshr performs MeSH-based annotation and overrepresentation analysis of gene lists to identify enriched Medical Subject Headings (MeSH) terms and complement Gene Ontology (GO) interpretations.

Key Features:

• Annotation Maps: Utilizes Medical Subject Headings (MeSH) to create detailed annotation maps that describe genes and datasets.
• Overrepresentation Analysis (ORA): Performs ORA by contrasting observed frequencies of MeSH terms in gene lists with background frequencies to identify significant terms.
• Comparison with Gene Ontology (GO): Compares MeSH ORA results with GO enrichment analysis to highlight overlapping and unique biological annotations.
• Unique MeSH Annotations: Identifies MeSH categories not covered by GO to expand and refine functional interpretations.

Scientific Applications:

• Functional Genomics: Highlights enriched biological themes and gene roles in gene-expression and gene-list analyses using MeSH terms.
• Livestock Genetics: Provides insights into the genetic basis of complex traits in species such as dairy cattle, swine, and horses.
• Annotation Integration: Enhances biological interpretation by integrating MeSH-based annotations with GO-based results.

Methodology:

Performs overrepresentation analysis by contrasting observed versus background frequencies of MeSH terms; compares MeSH ORA with GO enrichment analysis; demonstrated using three published datasets: a gene expression study in dairy cattle, SNP-based genome-wide prediction in swine, and identification of genomic regions targeted by selection in horses.