GeneShelf: a web-based visual interface for large gene expression time-series data repositories.
GeneShelf: a web-based visual interface for large gene expression time-series data repositories.
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GeneShelf：一个基于网络的大型基因表达时间序列数据存储库的可视化界面。
DOI：
10.1109/tvcg.2009.146
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发表时间：
2009
影响因子：
5.2
通讯作者：
Seo,Jinwook
中科院分区：
文献类型：
--
作者：
Kim,Bohyoung;Lee,Bongshin;Knoblach,Susan;Hoffman,Eric;Seo,Jinwook
高通量基因表达分析技术的广泛使用使生物医学研究界能够在网络上的许多公共数据库中共享大量基因表达数据集。然而，当前的基因表达数据存储库提供数据的静态表示并支持有限的交互。这阻碍了生物学家有效探索共享基因表达数据集。为了满足对更好的界面以提高公共数据集的实用性的日益增长的需求，我们设计并开发了一个新的基于网络的可视化界面，名为 GeneShelf (http://bioinformatics.cnmcresearch.org/GeneShelf)。它建立在可缩放网格显示的基础上来表示两个分类维度。它还结合了带有可扩展时间点的增强时间线，通过嵌入条形图更好地显示重点时间点的多个数据值。我们将 GeneShelf 应用到最大的微阵列数据集之一，用于研究小鼠和大鼠脊髓损伤的进展和恢复过程。我们与生物学家一起进行了案例研究和初步定性用户研究，以展示 GeneShelf 的实用性和可用性。
A widespread use of high-throughput gene expression analysis techniques enabled the biomedical research community to share a huge body of gene expression datasets in many public databases on the web. However, current gene expression data repositories provide static representations of the data and support limited interactions. This hinders biologists from effectively exploring shared gene expression datasets. Responding to the growing need for better interfaces to improve the utility of the public datasets, we have designed and developed a new web-based visual interface entitled GeneShelf (http://bioinformatics.cnmcresearch.org/GeneShelf). It builds upon a zoomable grid display to represent two categorical dimensions. It also incorporates an augmented timeline with expandable time points that better shows multiple data values for the focused time point by embedding bar charts. We applied GeneShelf to one of the largest microarray datasets generated to study the progression and recovery process of injuries at the spinal cord of mice and rats. We present a case study and a preliminary qualitative user study with biologists to show the utility and usability of GeneShelf.