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proteomics-enrichment

Perform pathway and functional enrichment analysis on proteomics data with STRING, DAVID, or g:Profiler.

155|26|Updated Mar 14, 2026
Search Tags:#functional analysis#pathway analysis#enrichment#proteomics#gene ontology#STRING#g:Profiler
One-click install
npx skills add https://github.com/TianGzlab/OmicsClaw --skill proteomics-enrichment
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: proteomics-enrichment
Source: https://github.com/TianGzlab/OmicsClaw/tree/main/skills/proteomics/proteomics-enrichment
Command: npx skills add https://github.com/TianGzlab/OmicsClaw --skill proteomics-enrichment

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

Interpreting large lists of proteins from experiments is challenging; this skill collapses hundreds of targets into a few meaningful biological pathways.

Core Features & Use Cases

  • Pathway Analysis: Perform Gene Ontology (GO) and pathway enrichment using established databases.
  • Network Visualization: Generate structural network graphs for enriched pathways.
  • Use Case: After identifying differentially expressed proteins, use this skill to understand the overarching biological processes or signaling pathways affected.

Quick Start

Run pathway enrichment on the provided list of significant proteins.

Frequently Asked Questions about proteomics-enrichment

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I perform pathway enrichment analysis on a list of differentially expressed proteins?▼

Pathway enrichment analysis maps your Uniprot IDs to Gene Symbols and executes hypergeometric tests over Kegg and Gene Ontology definitions to identify significantly affected biological processes.

What is the best way to visualize functional enrichment results for proteomics data?▼

Visualizing functional enrichment results involves generating structural network graphs for enriched pathways and tabulating key functionally enriched terms to uncover biological meaning in protein lists.

Can I use STRING, DAVID, or g:Profiler for gene ontology analysis of my protein targets?▼

Gene ontology analysis supports STRING, DAVID, and g:Profiler to perform pathway and functional enrichment, mapping your protein targets to known biological functions and signaling pathways.

Does the enrichment analysis support False Discovery Rate adjustments for multiple testing?▼

FDR multiple testing adjustments are supported and automatically applied to hypergeometric test results over known Kegg and Gene Ontology definitions to ensure statistically significant enriched terms.

What are the limitations of using DAVID versus g:Profiler for network visualization in proteomics?▼

Network visualization generates structural network graphs for enriched pathways, but specific functional coverage limitations between DAVID and g:Profiler depend on their respective underlying database definitions.

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