CyKEGGParser: tailoring KEGG pathways to fit into systems biology analysis workflows.
CyKEGGParser: tailoring KEGG pathways to fit into systems biology analysis workflows.
复制标题
DOI：
10.12688/f1000research.4410.2
复制
发表时间：
2014
期刊：
影响因子：
--
通讯作者：
Arakelyan A
中科院分区：
文献类型：
--
作者：
Nersisyan L;Samsonyan R;Arakelyan A
KEGG途径数据库是生物分子途径图的广泛接受的来源。在本文中，我们介绍了Cytoscape 3的CyKEGGParser应用程序（http：//apps.cytoscape.org/apps/cykeggparser），该应用程序允许使用KEGG通路图进行操作。沿着KGML和BioPAX格式的通路检索、可视化和导出的基本功能，该应用程序还提供了独特的功能，用于计算机辅助调整KEGG通路KGML文件中的不一致性，以及生成组织和蛋白质-蛋白质相互作用的特定通路。我们证明，使用CyKEGGParser创建的生物上下文特定的KEGG途径，使系统生物学分析更敏感和适当的原始途径相比。
The KEGG pathway database is a widely accepted source for biomolecular pathway maps. In this paper we present the CyKEGGParser app ( http://apps.cytoscape.org/apps/cykeggparser) for Cytoscape 3 that allows manipulation with KEGG pathway maps. Along with basic functionalities for pathway retrieval, visualization and export in KGML and BioPAX formats, the app provides unique features for computer-assisted adjustment of inconsistencies in KEGG pathway KGML files and generation of tissue- and protein-protein interaction specific pathways. We demonstrate that using biological context-specific KEGG pathways created with CyKEGGParser makes systems biology analysis more sensitive and appropriate compared to original pathways.