Gil Daniel P, Law Jeffrey N, Murali T M
Department of Computer Science, Virginia Tech, Blacksburg, USA.
Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, USA.
F1000Res. 2017 Jan 20;6:58. doi: 10.12688/f1000research.9909.1. eCollection 2017.
PathLinker is a graph-theoretic algorithm for reconstructing the interactions in a signaling pathway of interest. It efficiently computes multiple short paths within a background protein interaction network from the receptors to transcription factors (TFs) in a pathway. We originally developed PathLinker to complement manual curation of signaling pathways, which is slow and painstaking. The method can be used in general to connect any set of sources to any set of targets in an interaction network. The app presented here makes the PathLinker functionality available to Cytoscape users. We present an example where we used PathLinker to compute and analyze the network of interactions connecting proteins that are perturbed by the drug lovastatin.
PathLinker是一种用于重建感兴趣的信号通路中相互作用的图论算法。它能在背景蛋白质相互作用网络中高效计算从受体到通路中转录因子（TFs）的多条短路径。我们最初开发PathLinker是为了补充信号通路的人工整理，人工整理既缓慢又费力。该方法一般可用于在相互作用网络中连接任何一组源到任何一组目标。这里展示的应用程序使Cytoscape用户能够使用PathLinker功能。我们给出一个例子，在其中我们使用PathLinker来计算和分析连接受药物洛伐他汀干扰的蛋白质的相互作用网络。
