VisANT 3.0: new modules for pathway visualization, editing, prediction and construction
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction
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DOI：
10.1093/nar/gkm295
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发表时间：
2007-07-01
影响因子：
14.9
通讯作者：
DeLisi, Charles
中科院分区：
文献类型：
--
作者：
Hu, Zhenjun;Ng, David M.;DeLisi, Charles
VisANT 3.0集成了KEGG和Predictome数据库，以及使用斯坦福微阵列数据库（SMD）和Gene Expression Omnibus （GEO）数据库获得的数据集搜索共表达基因/蛋白质的两个搜索引擎，支持探索性途径分析，包括多种途径的多尺度可视化，使用KEGG兼容的可视化符号编辑和注释途径，以及途径背景下表达数据的可视化。表达式级别由颜色强度或具有嵌入表达式配置文件的节点表示。多个实验可以导航或动画。已知的KEGG通路可以通过查询已知通路成员的共表达成分或具有已知物理相互作用的蛋白质来丰富。功能未知的基因/蛋白的预测途径可以从共表达或物理相互作用数据中推断出来。VisANT生成的路径可以保存为计算机可读的XML格式（VisML）、图形图像或高分辨率可缩放矢量图形（SVG）。VisML格式的路径可以在感兴趣的组中安全地共享，或者使用简单的Web链接在线发布。VisANT可在http://visant.bu.edu免费获得。
With the integration of the KEGG and Predictome databases as well as two search engines for coexpressed genes/proteins using data sets obtained from the Stanford Microarray Database (SMD) and Gene Expression Omnibus (GEO) database, VisANT 3.0 supports exploratory pathway analysis, which includes multi-scale visualization of multiple pathways, editing and annotating pathways using a KEGG compatible visual notation and visualization of expression data in the context of pathways. Expression levels are represented either by color intensity or by nodes with an embedded expression profile. Multiple experiments can be navigated or animated. Known KEGG pathways can be enriched by querying either coexpressed components of known pathway members or proteins with known physical interactions. Predicted pathways for genes/proteins with unknown functions can be inferred from coexpression or physical interaction data. Pathways produced in VisANT can be saved as computer-readable XML format (VisML), graphic images or high-resolution Scalable Vector Graphics (SVG). Pathways in the format of VisML can be securely shared within an interested group or published online using a simple Web link. VisANT is freely available at http://visant.bu.edu.