原创力文档arena3d visualizing time-driven phenotypic differences in biological systemsarena3d可视化一个完全时间驱动表型差异的生物系统项目.pdfVIP
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arena3d visualizing time-driven phenotypic differences in biological systemsarena3d可视化一个完全时间驱动表型差异的生物系统项目
Secrier et al. BMC Bioinformatics 2012, 13:45
/1471-2105/13/45
SOFTWARE Open Access
Arena3D: visualizing time-driven phenotypic
differences in biological systems
Maria Secrier1*, Georgios A Pavlopoulos2,3, Jan Aerts2,3 and Reinhard Schneider1,4
Abstract
Background: Elucidating the genotype-phenotype connection is one of the big challenges of modern molecular
biology. To fully understand this connection, it is necessary to consider the underlying networks and the time
factor. In this context of data deluge and heterogeneous information, visualization plays an essential role in
interpreting complex and dynamic topologies. Thus, software that is able to bring the network, phenotypic and
temporal information together is needed. Arena3D has been previously introduced as a tool that facilitates link
discovery between processes. It uses a layered display to separate different levels of information while emphasizing
the connections between them. We present novel developments of the tool for the visualization and analysis of
dynamic genotype-phenotype landscapes.
Results: Version 2.0 introduces novel features that allow handling time course data in a phenotypic context. Gene
expression levels or other measures can be loaded and visualized at different time points and phenotypic
comparison is facilitated through clustering and correlation display or highlighting of impacting changes through
time. Similarity scoring allows the identification of global patterns in dynamic heterogeneous data. In this paper we
demonstrate the utility of the tool on two distinct biological problems of different scales. First, we analyze a medium
scale dataset that looks at perturbation effects of the pluripotency regulator Nanog in murine embryonic stem cells.
Dynamic cluster analysis suggests alternative indirect links between Nanog a
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