Can I analyze my own expression data with this skill?

Yes, you can submit TSV formatted expression data with quantitative values to identify significantly impacted pathways through the Analysis Service.

How can I visualize the results of my pathway analysis?

The skill can generate specific URLs using analysis tokens that allow you to view your results directly in the interactive Reactome Pathway Browser.

How long are analysis tokens valid?

Analysis tokens generated by the Reactome Analysis Service are valid for 7 days, allowing you to retrieve or share results without re-submitting data.

Does this skill support non-human species?

While Reactome focuses on human pathways, it provides species projection capabilities to map identifiers from other organisms to their human ortholog pathways.

What identifier types are supported by this skill?

It supports various formats including UniProt accessions, Gene symbols, Ensembl IDs, EntrezGene IDs, and ChEBI IDs for small molecules.

Reactome Biological Pathways

Name: Reactome Biological Pathways
Author: Zehong-Wang

byZehong-Wang

0•

Data Science & ML

Queries the Reactome database to perform biological pathway analysis, gene enrichment, and molecular interaction mapping for systems biology research.

This skill integrates the Reactome pathway database directly into your workflow, enabling seamless access to over 2,800 human biological pathways and curated molecular data. It allows researchers and bioinformaticians to perform overrepresentation analysis on gene lists, analyze expression data for pathway significance, and map molecular entities to specific biological processes. By leveraging the Reactome REST API and Python client, it facilitates complex systems biology studies, ranging from identifying disease-related mechanisms to generating visualization links for the Reactome Pathway Browser.

Key Features

01Map gene symbols, UniProt IDs, and Ensembl IDs to biological processes

02Compare biological pathways and projections across different species

03Perform overrepresentation and gene expression pathway enrichment analysis

04Generate visualization URLs for the interactive Reactome Pathway Browser

05Retrieve detailed pathway hierarchies, reactions, and molecular entities

060 GitHub stars

Use Cases

01Annotating gene lists from CRISPR screens or GWAS studies with functional pathway data

02Analyzing differential expression results to identify significantly affected biological pathways

03Investigating molecular interactions and protein complexes within specific disease models

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add zehong-wang/kosmos reactome-database

For use in Claude.ai and ChatGPT

Download Skill