meshes

meshes computes enrichment of gene lists or whole expression profiles using the National Library of Medicine Medical Subject Headings (MeSH) to quantify semantic similarities between individual genes and groups of genes.

Key Features:

• Enrichment Analysis: Performs enrichment analysis of gene lists or whole expression profiles using MeSH annotations of MEDLINE/PubMed-indexed articles.
• Semantic Comparisons: Computes quantitative semantic similarities between MeSH terms to assess similarity between individual genes and gene groups.
• Bioconductor Integration: Aligns with the Bioconductor framework for analysis of high-throughput genomic data in R.

Scientific Applications:

• Genomics and Molecular Biology: Identifies biological themes, pathways, and gene-function associations within large genomic datasets via MeSH-based enrichment and similarity metrics.
• Interdisciplinary Research: Enables semantic analysis of biomedical literature across domains by leveraging the MeSH controlled vocabulary for cross-disciplinary interpretation.

Methodology:

Uses the MeSH controlled vocabulary to index and analyze MEDLINE/PubMed literature for enrichment of gene lists or expression profiles and applies semantic-comparison metrics on MeSH terms to compute quantitative similarities between genes and gene groups.