SubpathwayMiner: a software package for flexible identification of pathways.
SubpathwayMiner: a software package for flexible identification of pathways.
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SubpathwayMiner：灵活识别路径的软件包
DOI：
10.1093/nar/gkp667
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发表时间：
2009-10
影响因子：
14.9
通讯作者：
Xu L
中科院分区：
文献类型：
--
作者：
Li C;Li X;Miao Y;Wang Q;Jiang W;Xu C;Li J;Han J;Zhang F;Gong B;Xu L
随着微阵列、质谱和大规模诱变等高通量实验技术的发展，自动标注基因集和识别相关途径的需求日益增加。虽然开发了许多通路分析工具，但仍然需要新的工具来满足灵活或高级分析目的的要求。在这里，我们开发了一个基于r的软件包（SubpathwayMiner），用于灵活的路径识别。SubpathwayMiner利用代谢途径的结构信息，实现对代谢途径的子途径识别。此外，SubpathwayMiner还在注释基因集和识别相关通路（整个通路和子通路）方面提供了更大的灵活性：(i) SubpathwayMiner能够为用户提供最新的通路分析结果；（ii） SubpathwayMiner支持KEGG基因数据库中的多种物种（约100种真核生物，714种细菌和52种古细菌）和不同的基因标识符（Entrez基因id， NCBI-gi id, UniProt id， PDB id等）；（iii）该系统在与其他基于r的生物学工具合作方面非常有效。SubpathwayMiner可以在http://cran.r-project.org/web/packages/SubpathwayMiner/免费获得。
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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DOI：
10.1073/pnas.011404098
发表时间：
2001-01-02
影响因子：
11.1
作者：
Li, C;Wong, WH
通讯作者：
Wong, WH
影响因子：
14.9
作者：
Goffard N;Weiller G
通讯作者：
Weiller G
影响因子：
14.9
作者：
Chung HJ;Park CH;Han MR;Lee S;Ohn JH;Kim J;Kim J;Kim JH
通讯作者：
Kim JH
影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
影响因子：
6.4
作者：
Chen, Yun-Ju;Chen, Chu;Wu, Ming-Tsang
通讯作者：
Wu, Ming-Tsang