Journal
NUCLEIC ACIDS RESEARCH
Volume 37, Issue 19, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkp667
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Funding
- National Natural Science Foundation of China [30871394, 30370798, 30571034]
- National High Tech Development Project of China
- 863 Program [2007AA02Z329]
- National Basic Research Program of China
- 973 Program [2008CB517302]
- National Science Foundation of Heilongjiang Province [ZJG0501, 1055HG009, GB03C602-4, BMFH060044]
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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 (similar to 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/.
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