Biran Hadas, Kupiec Martin, Sharan Roded
School of Electrical Engineering, Tel Aviv University, Tel Aviv, Israel.
School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel.
Front Genet. 2019 Jan 22;10:4. doi: 10.3389/fgene.2019.00004. eCollection 2019.
Network propagation is a central tool in biological research. While a number of variants and normalizations have been proposed for this method, each has its own shortcomings and no large scale assessment of those variants is available. Here we propose a novel normalization method for network propagation that is based on evaluating the propagation results against those obtained on randomized networks that preserve node degrees. In this way, our method overcomes potential biases of previous methods. We evaluate its performance on multiple large scale datasets and find that it compares favorably to previous approaches in diverse gene prioritization tasks. We further demonstrate its utility on a focused dataset of telomere length maintenance in yeast. The normalization method is available at http://anat.cs.tau.ac.il/WebPropagate.
网络传播是生物学研究中的核心工具。虽然针对该方法已经提出了许多变体和归一化方法，但每种方法都有其自身的缺点，并且没有对这些变体进行大规模评估。在此，我们提出一种用于网络传播的新型归一化方法，该方法基于将传播结果与在保留节点度的随机网络上获得的结果进行评估。通过这种方式，我们的方法克服了先前方法的潜在偏差。我们在多个大规模数据集上评估了其性能，发现在各种基因优先级排序任务中，它与先前的方法相比具有优势。我们进一步在酵母端粒长度维持的重点数据集上证明了其效用。该归一化方法可在http://anat.cs.tau.ac.il/WebPropagate获取。
