HGNChelper

HGNChelper validates and corrects human and mouse gene symbols by cross-referencing input identifiers against authoritative nomenclature to ensure use of current approved gene names.

Key Features:

• Species support: Validates and corrects gene symbols for human and mouse using species-specific authoritative sources.
• Identification of invalid symbols: Detects known aliases, outdated gene symbols, and common mislabeling errors including unintentional conversion of gene symbols into date formats by spreadsheet software.
• Correction mechanism: Suggests corrected, up-to-date approved gene symbols where mappings are available.
• Database integration: Cross-references gene symbols against the HUGO Gene Nomenclature Committee (HGNC) for human and Mouse Genome Informatics (MGI) for mouse.
• Prevalence analysis: Has been applied to the Molecular Signatures Database (mSigDB 7.0) and Gene Expression Omnibus platform annotation files, showing invalid symbol prevalence of roughly 3% in recent platforms and 30–40% in older 2002–2003 datasets.

Scientific Applications:

• Gene expression studies: Ensures input gene symbols are accurate for differential expression and other expression analyses.
• Pathway and signature analysis: Standardizes gene symbols for pathway enrichment and molecular signature comparisons.
• Genomics data curation: Improves annotation quality of platform files and curated gene sets used in molecular biology research.

Methodology:

Cross-references input gene symbols against HGNC and MGI, detects common mislabeling patterns (including spreadsheet-induced date conversions), and suggests corrections based on mappings from those authoritative sources.