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Nucleic Acids Research Advance Access originally published online on August 25, 2009
Nucleic Acids Research 2009 37(19):e131; doi:10.1093/nar/gkp667
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Nucleic Acids Research, 2009, Vol. 37, No. 19 e131
© The Author 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses?by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

SubpathwayMiner: a software package for flexible identification of pathways

Chunquan Li1, Xia Li1,*, Yingbo Miao1, Qianghu Wang1, Wei Jiang1, Chun Xu1,2, Jing Li1, Junwei Han1, Fan Zhang1, Binsheng Gong1 and Liangde Xu1

1College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, People's Republic of China and 2Princess Margaret Hospital in University Health Network, Toronto, Ontario M5G 2L7, Canada

*To whom correspondence should be addressed. Tel: +86 451 86615922; Fax: +86 451 86615922; Email: lixia{at}hrbmu.edu.cn

Received January 9, 2009. Revised July 27, 2009. Accepted July 29, 2009.

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 sub-pathway 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/.


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