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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
SubpathwayMiner: a software package for flexible identification of pathways.
Chunquan Li1, Xia Li, Yingbo Miao
1College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, People's Republic of China.
Nucleic Acids Research
|August 27, 2009
Summary
SubpathwayMiner is a new R package for flexible pathway identification and gene set annotation. It enables advanced analysis of metabolic pathways and sub-pathways across numerous species and gene identifiers.
Area of Science:
- Bioinformatics
- Computational Biology
- Systems Biology
Background:
- High-throughput techniques generate large gene sets requiring automated annotation and pathway identification.
- Existing pathway analysis tools may lack the flexibility for advanced or specific analytical needs.
Purpose of the Study:
- To develop a flexible R-based software package, SubpathwayMiner, for pathway and sub-pathway identification.
- To enhance gene set annotation and pathway analysis capabilities.
Main Methods:
- Utilized pathway structure information for sub-pathway identification.
- Developed an R-based software package for flexible pathway analysis.
- Integrated support for multiple species and various gene identifiers.
Main Results:
- SubpathwayMiner facilitates flexible identification of metabolic pathways and sub-pathways.
- The tool supports up-to-date pathway analysis for approximately 100 eukaryotes, 714 bacteria, and 52 Archaea.
- It accommodates diverse gene identifiers (e.g., Entrez Gene IDs, UniProt IDs) from the KEGG GENE database.
Conclusions:
- SubpathwayMiner offers a flexible and efficient solution for gene set annotation and pathway analysis.
- The package enhances the ability to identify entire pathways and specific sub-pathways.
- It is compatible with other R-based bioinformatics tools and freely available.
