Document Type
Article
Publication Date
2009
Abstract
With the development of high-throughput experimental techniques such as microarray, mass spectrometry and large-scale mutagenesis, there is an increasing need to automatically annotate gene sets and identify the involved pathways. Although many pathway analysis tools are developed, new tools are still needed to meet the requirements for flexible or advanced analysis purpose. Here, we developed an R-based software package (SubpathwayMiner) for flexible pathway identification. SubpathwayMiner facilitates subpathway identification of metabolic pathways by using pathway structure information. Additionally, SubpathwayMiner also provides more flexibility in annotating gene sets and identifying the involved pathways (entire pathways and sub-pathways): (i) SubpathwayMiner is able to provide the most up to- date pathway analysis results for users; (ii) SubpathwayMiner supports multiple species (~100 eukaryotes, 714 bacteria and 52 Archaea) and different gene identifiers (Entrez Gene IDs, NCBI-gi IDs, UniProt IDs, PDB IDs, etc.) in the KEGG GENE database; (iii) the system is quite efficient in cooperating with other R-based tools in biology. SubpathwayMiner is freely available at http://cran.r-project.org/web/packages/SubpathwayMiner/.
Recommended Citation
Li, C., Li, X., Miao, Y., Wang, Q., Jiang, W., Xu, C., Li, J., Han, J., Zhang, F., Gong, B., & Xu, L. (2009). SubpathwayMiner: a software package for flexible identification of pathways. Nucleic acids research, 37(19), e131. https://doi.org/10.1093/nar/gkp667
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial 3.0 License
Publication Title
Nucleic Acids Research
DOI
10.1093/nar/gkp667
Comments
Copyright The Author 2009. Published by Oxford University Press