Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.
Sci Signal. 2011 Oct 25;4(196):pl1. doi: 10.1126/scisignal.2001935.
Genome-scale screening studies are gradually accumulating a wealth of data on the putative involvement of hundreds of genes in various cellular responses or functions. A fundamental challenge is to chart the molecular pathways that underlie these systems. ANAT is an interactive software tool, implemented as a Cytoscape plug-in, for elucidating functional networks of proteins. It encompasses a number of network inference algorithms and provides access to networks of physical associations in several organisms. In contrast to existing software tools, ANAT can be used to infer subnetworks that connect hundreds of proteins to each other or to a given set of "anchor" proteins, a fundamental step in reconstructing cellular subnetworks. The interactive component of ANAT provides an array of tools for evaluating and exploring the resulting subnetwork models and for iteratively refining them. We demonstrate the utility of ANAT by studying the crosstalk between the autophagic and apoptotic cell death modules in humans, using a network of physical interactions. Relative to published software tools, ANAT is more accurate and provides more features for comprehensive network analysis. The latest version of the software is available at http://www.cs.tau.ac.il/~bnet/ANAT_SI.
基因组规模的筛选研究逐渐积累了大量数据，这些数据表明数百个基因参与了各种细胞反应或功能。一个基本的挑战是绘制这些系统所基于的分子途径图。ANAT 是一个交互式软件工具，作为 Cytoscape 插件实现，用于阐明蛋白质的功能网络。它包含了许多网络推断算法，并提供了对几种生物体中物理关联网络的访问。与现有的软件工具不同，ANAT 可用于推断将数百个蛋白质相互连接或连接到给定的“锚”蛋白质集的子网，这是重建细胞子网的基本步骤。ANAT 的交互组件提供了一系列工具，用于评估和探索由此产生的子网模型，并对其进行迭代优化。我们通过使用物理相互作用网络研究人类自噬和细胞凋亡模块之间的串扰，展示了 ANAT 的实用性。与已发表的软件工具相比，ANAT 更准确，并为全面的网络分析提供了更多功能。该软件的最新版本可在 http://www.cs.tau.ac.il/~bnet/ANAT_SI 上获得。
