Brohée Sylvain, Faust Karoline, Lima-Mendez Gipsi, Vanderstocken Gilles, van Helden Jacques
Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Campus Plaine, CP 263, Boulevard du Triomphe, Bruxelles, Belgium.
Nat Protoc. 2008;3(10):1616-29. doi: 10.1038/nprot.2008.100.
Network Analysis Tools (NeAT) is a suite of computer tools that integrate various algorithms for the analysis of biological networks: comparison between graphs, between clusters, or between graphs and clusters; network randomization; analysis of degree distribution; network-based clustering and path finding. The tools are interconnected to enable a stepwise analysis of the network through a complete analytical workflow. In this protocol, we present a typical case of utilization, where the tasks above are combined to decipher a protein-protein interaction network retrieved from the STRING database. The results returned by NeAT are typically subnetworks, networks enriched with additional information (i.e., clusters or paths) or tables displaying statistics. Typical networks comprising several thousands of nodes and arcs can be analyzed within a few minutes. The complete protocol can be read and executed in approximately 1 h.
网络分析工具（NeAT）是一套计算机工具，集成了多种用于生物网络分析的算法：图之间、簇之间或图与簇之间的比较；网络随机化；度分布分析；基于网络的聚类和路径查找。这些工具相互连接，以通过完整的分析工作流程对网络进行逐步分析。在本方案中，我们展示了一个典型的应用案例，其中上述任务被组合起来以解读从STRING数据库检索到的蛋白质-蛋白质相互作用网络。NeAT返回的结果通常是子网、富含额外信息（即簇或路径）的网络或显示统计数据的表格。包含数千个节点和弧的典型网络可在几分钟内进行分析。完整的方案大约可在1小时内阅读并执行完毕。
