Comparative study of computational methods for reconstructing genetic networks of cancer-related pathways.
Comparative study of computational methods for reconstructing genetic networks of cancer-related pathways.
复制标题
DOI：
10.4137/cin.s13781
复制
发表时间：
2014
影响因子：
2
通讯作者：
Shojaie A
中科院分区：
文献类型：
--
作者：
Sedaghat N;Saegusa T;Randolph T;Shojaie A
网络重构是系统生物学中一项重要而又具有挑战性的任务。虽然最近已经提出了许多方法来从不同的数据类型重建生物网络，估计网络的属性和重建方法之间的差异还没有得到很好的理解。在本文中，我们进行了一个全面的经验评估现有的七种网络重建方法，通过比较正常和肿瘤样本的不同稀疏水平的估计网络。结果表明，使用不同的重建方法重建的网络的实质性的异质性。我们的研究结果还提供了证据，正常和肿瘤样本的网络之间的显着差异，即使在占相当大的变化，使用不同的重建方法估计的网络结构。这些差异可以为与癌症发生和进展相关的遗传相互作用机制的变化提供新的见解。
Network reconstruction is an important yet challenging task in systems biology. While many methods have been recently proposed for reconstructing biological networks from diverse data types, properties of estimated networks and differences between reconstruction methods are not well understood. In this paper, we conduct a comprehensive empirical evaluation of seven existing network reconstruction methods, by comparing the estimated networks with different sparsity levels for both normal and tumor samples. The results suggest substantial heterogeneity in networks reconstructed using different reconstruction methods. Our findings also provide evidence for significant differences between networks of normal and tumor samples, even after accounting for the considerable variability in structures of networks estimated using different reconstruction methods. These differences can offer new insight into changes in mechanisms of genetic interaction associated with cancer initiation and progression.