TeaProt

TeaProt integrates transcription factor enrichment, gene set enrichment analysis, and pathway-level interpretation to analyze proteomics datasets and detect underrepresented post-translational modifications (PTMs).

Key Features:

• Integration with urPTMdb: Leverages curated substrate lists from urPTMdb focused on proteins modified by underrepresented PTMs to enable PTM-aware analyses.
• Upstream transcription factor enrichment: Performs enrichment analysis of transcription factors to identify potential regulators driving observed proteomic changes.
• Downstream pathway analysis: Conducts pathway-level interpretation to map proteomic alterations to biological pathways and processes.
• Gene Set Enrichment Analysis (GSEA): Supports GSEA using gene sets sourced from MSigDB, CHEA, and urPTMdb to detect enriched biological signatures.
• Comprehensive molecular annotations: Annotates proteins with drug–gene interactions, subcellular localization, phenotypic functions, gene–disease associations, and enzyme–gene interactions.
• Detection of unexpected PTM regulation: Identifies enrichments and substrate patterns indicative of underrepresented PTM regulation within experimental datasets.

Scientific Applications:

• Western diet–induced proteome remodeling: Revealed alterations in energy metabolism, interferon responses, adipogenesis, enrichment of HMGylation substrates, and transcriptional regulation involving PPARG and CEBPA.
• Interactome analysis of ADP-ribose glycohydrolase TARG1: Identified enrichment of ADP-ribosylation and associated proteins localized to nucleoli and the endoplasmic reticulum.

Methodology:

Performs upstream transcription factor enrichment and downstream pathway analysis, executes GSEA with MSigDB, CHEA, and urPTMdb gene sets, integrates curated PTM substrate information from urPTMdb, and annotates proteins with drug–gene interactions, subcellular localization, phenotypic functions, gene–disease associations, and enzyme–gene interactions.