PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data
PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data
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DOI：
10.1093/bioinformatics/btx149
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发表时间：
2017-07-15
期刊：
影响因子：
5.8
通讯作者：
Schultz, Nikolaus
中科院分区：
文献类型：
--
作者：
Bahceci, Istemi;Dogrusoz, Ugur;Schultz, Nikolaus
动机：虽然现有的网络可视化工具可以探索癌症基因组学数据，但大多数生物学家更喜欢简化的路径图，例如癌症基因组图谱（TCGA）中的许多手稿中的路径图。这些通路图通常总结了通路在个体癌症类型中如何改变，包括每个基因的改变频率。结果：为了满足这一需求，我们开发了基于Web的工具PathwayMapper，它可以在大多数常见的Web浏览器中运行。它可用于查看预先策划的癌症途径，或作为创建新途径的图形编辑器，能够覆盖来自cBioPortal的基因组改变数据。此外，还提供了一种协作模式，允许科学家在构建路径上进行交互式合作，支持并发修改和内置冲突解决方案。
Motivation: While existing network visualization tools enable the exploration of cancer genomics data, most biologists prefer simplified, curated pathway diagrams, such as those featured in many manuscripts from The Cancer Genome Atlas (TCGA). These pathway diagrams typically summarize how a pathway is altered in individual cancer types, including alteration frequencies for each gene. Results: To address this need, we developed the web-based tool PathwayMapper, which runs in most common web browsers. It can be used for viewing pre-curated cancer pathways, or as a graphical editor for creating new pathways, with the ability to overlay genomic alteration data from cBioPortal. In addition, a collaborative mode is available that allows scientists to co-operate interactively on constructing pathways, with support for concurrent modifications and built-in conflict resolution.