Ranking Novel Regulatory Genes in Gene Expression Profiles using NetExpress.
Ranking Novel Regulatory Genes in Gene Expression Profiles using NetExpress.
复制标题
使用 NetExpress 对基因表达谱中的新型调控基因进行排名。
DOI：
10.1145/3019612.3021289
复制
发表时间：
2017
期刊：
影响因子：
--
通讯作者：
Jamil,HasanM
中科院分区：
文献类型：
--
作者：
Yelbay,Belma;Gow,Alexander;Jamil,HasanM
通过识别基因产物并确定它们在调控网络中的作用来理解基因调控是一个复杂的过程。一种常见的计算方法是从基因表达谱中反向工程一个调控网络，并使用有关基因、它们的相互作用和其他属性的已知信息来净化网络，以过滤掉不太可能的相互作用者。不幸的是，由于资源有限，大多数基因表达研究的时间点有限且数量较少，并且大多数逆向工程工具无法处理大量基因。这两个因素在影响过程的准确性方面都起着重要作用。在本文中，我们提出了一种新的基因排序算法，从基因表达谱与少量的时间点，使最相关的基因可以选择用于逆向工程。我们还提出了一个图形界面称为NetExpress，它采用了这种算法，并允许用户设置控制参数，以影响所需的结果，并可视化的分析迭代微调。
Understanding gene regulation by identifying gene products and determining their roles in regulatory networks is a complex process. A common computational method is to reverse engineer a regulatory network from gene expression profile, and sanitize the network using known information about the genes, their interactions and other properties to filter out unlikely interactors. Unfortunately, due to limited resources most gene expression studies have a limited and small number of time points, and most reverse engineering tools are unable to handle large numbers of genes. Both of these factors play significant roles in influencing the accuracy of the process. In this paper, we present a new gene ranking algorithm from gene expression profiles with a small number of time points so that the most relevant genes can be selected for reverse engineering. We also present a graphical interface calledNetExpress,which adopts this algorithm and allows users to set control parameters to effect the desired outcome, and visualize the analysis for iterative fine tuning.