Vials: Visualizing Alternative Splicing of Genes.
Vials: Visualizing Alternative Splicing of Genes.
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DOI：
10.1109/tvcg.2015.2467911
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发表时间：
2016-01
影响因子：
5.2
通讯作者：
Lex A
中科院分区：
文献类型：
--
作者：
Strobelt H;Alsallakh B;Botros J;Peterson B;Borowsky M;Pfister H;Lex A
选择性剪接是一个过程，通过这个过程，相同的DNA序列被用来组装不同的蛋白质，称为蛋白质异构体。选择性剪接通过选择性地省略一些通常与基因相关的编码区（外显子）来起作用。选择性剪接的检测是困难的，并且使用先进的数据采集方法和统计推断的组合。有关异构体丰度的知识对于理解正常过程和疾病以及最终通过靶向治疗改善治疗都很重要。然而，数据是复杂的，并且目前异构体的可视化既不具有感知效率也不具有可扩展性。为了解决这个问题，我们开发了Vial，这是一种新颖的视觉分析工具，使分析人员能够探索科学家用来判断亚型的各种数据集：与基因编码区相关的读数的丰度，连接的证据，即，连接编码区的边缘和同种型频率的预测。小瓶可扩展，因为它允许同时分析多组中的许多样品。因此，我们的工具使专家能够（a）识别样品组中的异构体丰度模式和（B）评估数据的质量。我们证明了我们的工具的价值，在案例研究中使用公开的数据集。
Alternative splicing is a process by which the same DNA sequence is used to assemble different proteins, called protein isoforms. Alternative splicing works by selectively omitting some of the coding regions (exons) typically associated with a gene. Detection of alternative splicing is difficult and uses a combination of advanced data acquisition methods and statistical inference. Knowledge about the abundance of isoforms is important for understanding both normal processes and diseases and to eventually improve treatment through targeted therapies. The data, however, is complex and current visualizations for isoforms are neither perceptually efficient nor scalable. To remedy this, we developed Vials, a novel visual analysis tool that enables analysts to explore the various datasets that scientists use to make judgments about isoforms: the abundance of reads associated with the coding regions of the gene, evidence for junctions, i.e., edges connecting the coding regions, and predictions of isoform frequencies. Vials is scalable as it allows for the simultaneous analysis of many samples in multiple groups. Our tool thus enables experts to (a) identify patterns of isoform abundance in groups of samples and (b) evaluate the quality of the data. We demonstrate the value of our tool in case studies using publicly available datasets.