enRoute: Dynamic path extraction from biological pathway maps for in-depth experimental data analysis
enRoute: Dynamic path extraction from biological pathway maps for in-depth experimental data analysis
复制标题
enRoute：从生物通路图中提取动态路径，以进行深入的实验数据分析
DOI：
10.1109/biovis.2012.6378600
复制
发表时间：
2012
期刊：
影响因子：
--
通讯作者：
D. Schmalstieg
中科院分区：
文献类型：
--
作者：
C. Partl;Denis Kalkofen;A. Lex;K. Kashofer;M. Streit;D. Schmalstieg
当分析生物过程实验数据的功能含义时，通路图是一个重要的信息来源。然而，将大量数据与路径图上的节点相关联并同时允许进行深度分析是一项具有挑战性的任务。虽然存在各种各样的方法来做到这一点，但它们要么不能扩展到少数实验之外，要么不能适当地表示途径。为了解决这个问题，我们引入了enRoute，这是一种新的方法，用于沿着从路径中动态提取的路径交互式探索实验数据。通过将提取的路径与实验数据并排显示，enRoute可以为每个路径节点提供大量数据。它可以可视化数百个样本，数十个实验条件，甚至同时捕获节点的不同方面的多个数据集。这种方法的另一个重要特性是它与任意形式的路径在概念上的兼容性。最值得注意的是，enRoute可以很好地处理手动创建的路径，因为它们可以在大型公共路径数据库中使用。我们使用来自完善的KEGG数据库的通路和表达，以及来自人类和小鼠的1000多个实验的拷贝数数据集来演示enRoute。我们通过与领域专家的案例研究来验证enRoute，这些专家使用enRoute来探索人类多形性胶质母细胞瘤和小鼠脂肪性肝炎模型的数据。
Pathway maps are an important source of information when analyzing functional implications of experimental data on biological processes. However, associating large quantities of data with nodes on a pathway map and allowing in depth-analysis at the same time is a challenging task. While a wide variety of approaches for doing so exist, they either do not scale beyond a few experiments or fail to represent the pathway appropriately. To remedy this, we introduce enRoute, a new approach for interactively exploring experimental data along paths that are dynamically extracted from pathways. By showing an extracted path side-by-side with experimental data, enRoute can present large amounts of data for every pathway node. It can visualize hundreds of samples, dozens of experimental conditions, and even multiple datasets capturing different aspects of a node at the same time. Another important property of this approach is its conceptual compatibility with arbitrary forms of pathways. Most notably, enRoute works well with pathways that are manually created, as they are available in large, public pathway databases. We demonstrate enRoute with pathways from the well-established KEGG database and expression as well as copy number datasets from humans and mice with more than 1,000 experiments. We validate enRoute using case studies with domain experts, who used enRoute to explore data for glioblastoma multiforme in humans and a model of steatohepatitis in mice.
DOI：
10.1109/tvcg.2011.250
发表时间：
2011-12-01
影响因子：
5.2
作者：
Lex, Alexander;Schulz, Hans-Joerg;Schmalstieg, Dieter
通讯作者：
Schmalstieg, Dieter
影响因子：
50.3
作者：
Verhaak RG;Hoadley KA;Purdom E;Wang V;Qi Y;Wilkerson MD;Miller CR;Ding L;Golub T;Mesirov JP;Alexe G;Lawrence M;O'Kelly M;Tamayo P;Weir BA;Gabriel S;Winckler W;Gupta S;Jakkula L;Feiler HS;Hodgson JG;James CD;Sarkaria JN;Brennan C;Kahn A;Spellman PT;Wilson RK;Speed TP;Gray JW;Meyerson M;Getz G;Perou CM;Hayes DN;Cancer Genome Atlas Research Network
通讯作者：
Cancer Genome Atlas Research Network
影响因子：
50.3
作者：
Noushmehr H;Weisenberger DJ;Diefes K;Phillips HS;Pujara K;Berman BP;Pan F;Pelloski CE;Sulman EP;Bhat KP;Verhaak RG;Hoadley KA;Hayes DN;Perou CM;Schmidt HK;Ding L;Wilson RK;Van Den Berg D;Shen H;Bengtsson H;Neuvial P;Cope LM;Buckley J;Herman JG;Baylin SB;Laird PW;Aldape K;Cancer Genome Atlas Research Network
通讯作者：
Cancer Genome Atlas Research Network