基于整数规划的信号通路完成方法及其在结直肠癌分析中的应用。

Takeyuki Tamura, Yoshihiro Yamanishi, Mao Tanabe, Susumu Goto, Minoru Kanehisa, Katsuhisa Horimoto, Tatsuya Akutsu
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引用次数: 0

摘要

信号通路通常由网络表示,其中每个节点对应一个蛋白质,每个边缘对应节点之间的关系,如激活、抑制和结合。然而,细胞中的这种信号通路可能受到遗传和表观遗传改变的影响。一些边可能被删除,一些边可能被新添加。目前关于已知信号通路的知识可以从一些公共数据库中获得,但大多数信号通路包括细胞状态改变的变化在很大程度上仍然未知。在本文中,我们开发了一种基于整数规划的方法,通过使用基因表达数据来推断这种变化。我们测试了我们的方法在KEGG数据库中重建结直肠癌通路的能力。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Integer programming-based method for completing signaling pathways and its application to analysis of colorectal cancer.

Signaling pathways are often represented by networks where each node corresponds to a protein and each edge corresponds to a relationship between nodes such as activation, inhibition and binding. However, such signaling pathways in a cell may be affected by genetic and epigenetic alteration. Some edges may be deleted and some edges may be newly added. The current knowledge about known signaling pathways is available on some public databases, but most of the signaling pathways including changes upon the cell state alterations remain largely unknown. In this paper, we develop an integer programming-based method for inferring such changes by using gene expression data. We test our method on its ability to reconstruct the pathway of colorectal cancer in the KEGG database.

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