Lu Long J, Sboner Andrea, Huang Yuanpeng J, Lu Hao Xin, Gianoulis Tara A, Yip Kevin Y, Kim Philip M, Montelione Gaetano T, Gerstein Mark B
Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA.
Trends Biochem Sci. 2007 Jul;32(7):320-31. doi: 10.1016/j.tibs.2007.06.003. Epub 2007 Jun 20.
Pathways are integral to systems biology. Their classical representation has proven useful but is inconsistent in the meaning assigned to each arrow (or edge) and inadvertently implies the isolation of one pathway from another. Conversely, modern high-throughput (HTP) experiments offer standardized networks that facilitate topological calculations. Combining these perspectives, classical pathways can be embedded within large-scale networks and thus demonstrate the crosstalk between them. As more diverse types of HTP data become available, both perspectives can be effectively merged, embedding pathways simultaneously in multiple networks. However, the original problem still remains - the current edge representation is inadequate to accurately convey all the information in pathways. Therefore, we suggest that a standardized and well-defined edge ontology is necessary and propose a prototype as a starting point for reaching this goal.
通路对于系统生物学至关重要。其经典表示法已被证明是有用的,但在赋予每个箭头(或边)的含义上并不一致,并且无意中暗示了一条通路与另一条通路的孤立。相反,现代高通量(HTP)实验提供了便于进行拓扑计算的标准化网络。结合这些观点,经典通路可以嵌入大规模网络中,从而展示它们之间的相互作用。随着更多类型的高通量数据可用,这两种观点可以有效融合,将通路同时嵌入多个网络中。然而,最初的问题仍然存在——当前的边表示法不足以准确传达通路中的所有信息。因此,我们建议需要一个标准化且定义明确的边本体,并提出一个原型作为实现这一目标的起点。