Can I visualize the analysis results?

The skill helps generate specific URLs containing analysis tokens that allow you to visualize your results directly in the Reactome Pathway Browser.

Does this skill support gene expression data?

Yes, it provides tools to submit TSV formatted expression data for quantitative pathway analysis and identifies relevant biological pathways based on expression values.

Which biological identifiers are supported?

Reactome supports a wide range of identifiers including UniProt accessions, Gene Symbols, Ensembl IDs, EntrezGene IDs, and ChEBI IDs for small molecules.

What is the Reactome Database skill used for?

It is used to query curated biological pathway data, perform enrichment analysis on gene or protein lists, and explore molecular interactions via the Reactome REST API.

Reactome Database

Name: Reactome Database
Author: x-cmd

byx-cmd

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Data Science & ML

Queries the Reactome REST API for pathway analysis, gene enrichment, and molecular interaction mapping in systems biology studies.

About

This skill empowers researchers and developers to integrate Reactome's peer-reviewed pathway database directly into AI-driven workflows. It provides specialized support for performing overrepresentation analysis, mapping gene lists to biological processes, and retrieving detailed information on molecular reactions and complexes. By leveraging both the Content and Analysis REST APIs, it simplifies complex bioinformatics tasks like species projection and expression data visualization, making it an essential tool for computational biology, drug discovery, and genomic research.

Key Features

8 GitHub stars
Pathway enrichment and overrepresentation analysis
Support for expression data and species projection
Automated result visualization in Reactome Pathway Browser
Gene and protein mapping to biological pathways
REST API integration for Content and Analysis services

Use Cases

Analyzing large-scale gene expression datasets for pathway relevance
Programmatically querying molecular interactions and entity hierarchies
Identifying statistically significant biological pathways from gene lists

About

Key Features

8 GitHub stars
Pathway enrichment and overrepresentation analysis
Support for expression data and species projection
Automated result visualization in Reactome Pathway Browser
Gene and protein mapping to biological pathways
REST API integration for Content and Analysis services

Use Cases

Analyzing large-scale gene expression datasets for pathway relevance
Programmatically querying molecular interactions and entity hierarchies
Identifying statistically significant biological pathways from gene lists