SubpathwayMiner: a software package for flexible identification of pathways. Export

@article{citeulike:5655355, 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 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 ( approximately 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/.}, author = {Li, Chunquan and Li, Xia and Miao, Yingbo and Wang, Qianghu and Jiang, Wei and Xu, Chun and Li, Jing and Han, Junwei and Zhang, Fan and Gong, Binsheng and Xu, Liangde}, citeulike-article-id = {5655355}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkp667}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/content/gkp667v1/.abstract}, citeulike-linkout-2 = {http://nar.oxfordjournals.org/content/gkp667v1/.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19706733}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19706733}, day = {25}, doi = {10.1093/nar/gkp667}, issn = {1362-4962}, journal = {Nucleic acids research}, keywords = {metabolic\_engineering, opensource, pathway, r, sbml, software}, month = {October}, number = {19}, pages = {gkp667+}, posted-at = {2009-10-20 11:23:08}, priority = {2}, title = {SubpathwayMiner: a software package for flexible identification of pathways.}, url = {http://dx.doi.org/10.1093/nar/gkp667}, volume = {37}, year = {2009} }

TY - JOUR ID - citeulike:5655355 L3 - citeulike-article-id:5655355 N2 - 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 ( approximately 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/. IS - 19 JF - Nucleic acids research SN - 1362-4962 TI - SubpathwayMiner: a software package for flexible identification of pathways. VL - 37 SP - gkp667 KW - metabolic_engineering KW - opensource KW - pathway KW - r KW - sbml KW - software AU - Li, Chunquan AU - Li, Xia AU - Miao, Yingbo AU - Wang, Qianghu AU - Jiang, Wei AU - Xu, Chun AU - Li, Jing AU - Han, Junwei AU - Zhang, Fan AU - Gong, Binsheng AU - Xu, Liangde PY - 2009/10/25/ UR - http://dx.doi.org/10.1093/nar/gkp667 ER -