Taylor Avigail, Steinberg Julia, Andrews Tallulah S, Webber Caleb
MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK and The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK and The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK and The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
Bioinformatics. 2015 Feb 1;31(3):442-4. doi: 10.1093/bioinformatics/btu669. Epub 2014 Oct 14.
We present GeneNet Toolbox for MATLAB (also available as a set of standalone applications for Linux). The toolbox, available as command-line or with a graphical user interface, enables biologists to assess connectivity among a set of genes of interest ('seed-genes') within a biological network of their choosing. Two methods are implemented for calculating the significance of connectivity among seed-genes: 'seed randomization' and 'network permutation'. Options include restricting analyses to a specified subnetwork of the primary biological network, and calculating connectivity from the seed-genes to a second set of interesting genes. Pre-analysis tools help the user choose the best connectivity-analysis algorithm for their network. The toolbox also enables visualization of the connections among seed-genes. GeneNet Toolbox functions execute in reasonable time for very large networks (∼10 million edges) on a desktop computer.
GeneNet Toolbox is open source and freely available from http://avigailtaylor.github.io/gntat14.
Supplementary data are available at Bioinformatics online.
我们展示了用于MATLAB的基因网络工具箱（也可作为一组适用于Linux的独立应用程序获取）。该工具箱有命令行版本或图形用户界面版本，使生物学家能够在他们选择的生物网络中评估一组感兴趣的基因（“种子基因”）之间的连通性。实现了两种计算种子基因之间连通性显著性的方法：“种子随机化”和“网络置换”。选项包括将分析限制在主要生物网络的指定子网络内，以及计算从种子基因到第二组感兴趣基因的连通性。预分析工具可帮助用户为其网络选择最佳的连通性分析算法。该工具箱还能可视化种子基因之间的连接。对于非常大的网络（约1000万条边），基因网络工具箱函数在台式计算机上能在合理时间内执行。
基因网络工具箱是开源的，可从http://avigailtaylor.github.io/gntat14免费获取。
补充数据可在《生物信息学》在线获取。
