aGOtool

aGOtool performs protein-abundance–aware Gene Ontology and UniProt keyword enrichment for post-translational modification (PTM) datasets to correct mass-spectrometry–based detection bias and reveal PTM-specific functional signals.

Key Features:

• Protein-abundance–aware enrichment: Performs GO and UniProt keyword enrichment that weights background term frequencies by protein abundance distributions.
• Statistical abundance correction: Implements a statistical correction that reweights GO-term frequencies according to protein abundance to reduce bias from highly expressed proteins.
• Proteome binning: Partitions the proteome into abundance bins and reweights GO-term associations in proportion to the frequency of modification in each bin.
• Abundance-corrected reference distribution: Generates an abundance-corrected reference distribution for enrichment testing.
• PTM type support: Supports analysis of multiple PTM types, including phosphorylation, ubiquitination, acetylation, and succinylation.
• Background comparisons: Enables comparisons of enrichment results across genome, observed proteome, and abundance-corrected backgrounds.
• Bias reduction and sensitivity: Reduces false enrichment driven by sampling bias in mass-spectrometry–based PTM identification and enhances detection of PTM-specific and under-represented functional categories.

Scientific Applications:

• PTM-specific functional inference: Distinguishing PTM-associated biological processes from artifacts of protein abundance in proteomics datasets.
• Comparative PTM analysis: Comparing enrichment across different PTM types and across genome, observed proteome, and abundance-corrected backgrounds to identify PTM-specific or shared functions.
• Reproducible PTM annotation: Supporting reproducible functional annotation of PTMs across diverse organisms and cell types.

Methodology:

Partitions the proteome into abundance bins, reweights GO-term associations proportional to the frequency of modification in each bin, and constructs an abundance-corrected reference distribution for enrichment analysis.