KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor.
KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor.
复制标题
DOI：
10.1093/bioinformatics/btp167
复制
发表时间：
2009-06-01
期刊：
影响因子：
--
通讯作者：
Wiemann S
中科院分区：
文献类型：
--
作者：
Zhang JD;Wiemann S
动机：KEGG PATHWAY是京都基因和基因组百科全书（KEGG）的一项服务，构建人工策划的通路图，以图形模型表示生物网络的当前知识。虽然在R/Bioconductor中已经实现了有价值的图形工具，但据我们所知，目前还没有软件包可以用图论解析和分析KEGG通路。结果如下：我们介绍了R和Bioconductor中的软件包KEGGgraph，KEGG途径和图形模型之间的接口以及这些图形的工具集。上级现有的方法，KEGGgraph捕获通路拓扑结构，并允许进一步分析或解剖通路图。我们通过分析人类胰腺癌通路的案例研究来展示该软件包的使用。可用性：KEGGgraph可在Bioconductor网站（http：//www.example.com）上免费获得。www.bioconductor.org KGML文件可从KEGG FTP站点（ftp：//ftp.genome.jp/pub/kegg/xml）下载。联系人：j.zhang@ dkfz-heidelberg.de补充信息：补充数据可在生物信息学在线获得。
Motivation: KEGG PATHWAY is a service of Kyoto Encyclopedia of Genes and Genomes (KEGG), constructing manually curated pathway maps that represent current knowledge on biological networks in graph models. While valuable graph tools have been implemented in R/Bioconductor, to our knowledge there is currently no software package to parse and analyze KEGG pathways with graph theory. Results: We introduce the software package KEGGgraph in R and Bioconductor, an interface between KEGG pathways and graph models as well as a collection of tools for these graphs. Superior to existing approaches, KEGGgraph captures the pathway topology and allows further analysis or dissection of pathway graphs. We demonstrate the use of the package by the case study of analyzing human pancreatic cancer pathway. Availability:KEGGgraph is freely available at the Bioconductor web site (http://www.bioconductor.org). KGML files can be downloaded from KEGG FTP site (ftp://ftp.genome.jp/pub/kegg/xml). Contact: j.zhang@dkfz-heidelberg.de Supplementary information: Supplementary data are available at Bioinformatics online.